Research Computing Center Wiki - User contributions [en]

Quick Reference Guide

2022-11-09T13:25:03Z

Karen: Software section

=Linux=
Below are the minimum Linux definitions, commands, and shortcuts that you should know to do work on an HPC cluster.
==Definitions==
1. '''Command''' - Word or letters typed into a terminal to make a computer do something. Executed by pressing enter after typing the command.

2. '''Command line''' - Literally, the line on which your cursor is on in the terminal. Sometimes used to describe the whole experience of not a graphical user interface, i.e. "Command Line Interface" or "CLI".

3. '''Command prompt''' - The text at the beginning of the command line, before your cursor. Typically [''username''@''computername''].

4. '''Directory''' - Another word for "Folder" (just like a folder in Windows or Mac). Often shortened to "dir" in commands, documentation, conversation, etc...

5. '''Terminal''' - Category of software that allows you to interact with your computer via commands, and can allow you to connect to a remote computer (via a CLI).

6. '''Path''' - The location of a file or directory. A series of subsequent directories to get to some file or directory. e.g., /home/john/file.txt

7. '''First /''' (in a path) - The root directory, where everything starts in the Linux file system.

8. '''Absolute path''' - a path that is written beginning with / (root)

9. '''Relative path''' - a path that is written relative to some other directory (does not begin with /)

10. (Command) '''Option''' - extra letter or word (-''SomeLetter'' or --''SomeWord'') put after a command to modify its behavior.
----
==Commands==
<big>'''Getting Help'''</big> (most important)
{| class="wikitable"
! Command !! Description !! Examples
|-
| <code>''command'' --help</code> || Print a commands help output to the terminal || <code>ls --help</code>
|-
| <code>man ''command''</code> || Read a command's manual (press q to exit) || <code>man ls</code>
|-
|}
<big>'''Directories'''</big>
{| class="wikitable"
! Command !! Description !! Examples
|-
| <code>ls</code> || List the contents of a particular directory (current dir if no path specified) || <code>ls /scratch/'''MyID'''</code>
|-
| <code>mkdir</code> || Make a new directory at the specified path || <code>mkdir /scratch/'''MyID'''/workdir</code>
|-
| <code>cd</code> || Change directory to a particular directory (personal /home dir if no path specified) || <code>cd /scratch/'''MyID'''/workdir</code>
|-
| <code>rmdir</code> || Remove an empty directory || <code>rmdir tmpdir</code>
|}
<big>'''Files'''</big>
{| class="wikitable"
|-
! Command !! Description !! Examples
|-
| <code>nano</code> || Create or edit a file with nano (to save and exit: ctrl + x, y, enter)|| <code>nano sub.sh</code>
|-
| <code>cat</code> || Print the contents of a file to the terminal (better for shorter files) || <code>cat slurm-42342.out</code>
|-
| <code>less</code> || View the contents of a file (better for longer files) || <code>less slurm-42342.out</code>
|-
| <code>cp</code> || Copy a file or files (<code>cp ''sourcepath(s) destinationpath''</code>) || <code>cp /scratch/'''MyID'''/workdir/sub.sh /work/'''labgroup'''</code>
|-
| <code>mv</code> || Move a file or files (<code>mv ''sourcepath(s) destinationpath''</code>) || <code>mv /scratch/'''MyID'''/workdir/sub.sh /work/'''labgroup'''</code>
|-
| <code>rm</code> || Remove a file or files || <code>rm oldfile.txt</code>
|-
| <code>rm -r</code> || Remove a directory and '''all''' of its contents, recursively (starting with the last dir in the path)|| <code>rm -r /home/'''MyID'''/olddir</code>
|-
| <code>dos2unix</code> || Removes DOS/Windows line endings in file || <code>dos2unix file.txt</code>
|-
| <code>mac2unix</code> || Removes Mac line endings in file. || <code>mac2unix file.txt</code>
|-
|}

<big>'''Software'''</big>
{| class="wikitable"
|-
!Command!!Description!!Examples
|-
|<code>ml spider <software name></code>||See if a software is available, will also show you which versions are available||<code>ml spider Blast+</code>
|-
|<code>ml <software name></code>||Load a software module||<code>ml BLAST+/2.12.0-gompi-2020b</code>
|-
|}
Also see the [[Software]] page and [[Frequently Asked Questions#Software|Software]] section of our FAQ.
----
[[#top|Back to Top]]
==Shortcuts ==

'''Linux'''

{| class="wikitable"
|-
!Shortcut!! Description
|-
| ctrl + l (lowercase L)||Clear your terminal screen (scroll up to see previous output)
|-
|up/down arrow keys||Cycle through previously entered commands
|-
|tab||auto-complete a file or directory name when typing a path (tab tab if more than one file begins with the letters you've typed)
|-
|esc, . (escape, then period)||Cycle through previous arguments to commands
|-
|ctrl + w||Backspace typed text on the command line, one word at a time
|-
|ctrl + c|| Cancel typed text on the command line
|-
|}

'''less'''

{| class="wikitable"
|-
!Shortcut!!Description
|-
| shift + g ||Go to the end of file
|-
|gg||Go to the beginning of file
|-
| -N then enter ||Display/hide line numbers
|-
|/''SomePattern''||Search forward through a file for ''SomePattern'' (/ then enter to keep searching forward for the same pattern)
|-
|?''SomePattern''||Search backwards through a file for ''SomePattern'' (? then enter to keep searching forward for the same pattern)
|-
|q ||Exit less
|-
|}
----
[[#top|Back to Top]]

=Slurm=
Below are the minimum Slurm commands that you should know to do work on an HPC cluster. The first table are default Slurm commands. The next table are GACRC pre-formatted wrapper scripts of the Slurm commands to provide more information and flexibility.
 
 
'''Default Slurm Commands'''
{| class="wikitable"
!Command!!Description!!Examples
|-
|<code>sbatch</code>|| Submit a submission script to the cluster||<code>sbatch sub.sh</code>
|-
|<code>squeue</code>||Check status currently running jobs (--me for only your jobs)||<code>squeue --me</code>
|-
|<code>sacct -X</code>||Check status of your jobs started since midnight of current day (-X for one line per job)||<code>sacct -X</code>
|-
|<code>sacct -X -S yyyy-mm-dd</code>||Check status of your jobs since yyyy-mm-dd||<code>sacct -X -S 2021-10-20</code>
|-
|<code>sacct -j ''jobID'' ||Check status of a particular job||<code>sacct -j 234213</code>
|-
|<code>scancel ''jobID'' ||Cancel one of your running jobs ||<code>scancel 456781</code>
|-
|<code>sinfo</code>||Check the status of partitions||<code>sinfo -p batch</code>
|-
|}
'''GACRC Slurm Commands'''
{| class="wikitable"
!Command!!Description/Slurm Equivalent!!Examples
|-
|<code>interact</code>||Start an interactive job. (Same as <code>qlogin</code> but with more flexibility)||<code>interact -c 4 --mem 10gb --time 01:00:00</code>
|-
|<code>sq</code>||<code>squeue</code>||<code>sq --me</code>
|-
|<code>sacct-gacrc -X</code>||<code>sacct</code>||<code>sacct-gacrc -X</code>
|-
|}

DRAM-bio-Sapelo2

2022-11-07T19:17:28Z

Karen: add --threads to example command

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
1.4.0

=== Author / Distributor ===

Please see https://github.com/WrightonLabCSU/DRAM

=== Description ===
DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs. DRAM annotates MAGs and viral contigs using KEGG (if provided by the user), UniRef90, PFAM, dbCAN, RefSeq viral, VOGDB and the MEROPS peptidase database as well as custom user databases.

The databases DRAM uses are already available on Sapelo2 in /db/DRAM_data/20222204/.

The database locations should be preset in the config file for DRAM-bio, you do not need to download them.

=== Running Program ===

* Version 1.4.0 is installed at /apps/eb/DRAM-bio/1.4.0/

To use version 1.4.0, please load the module with
<pre class="gscript">
ml DRAM-bio/1.4.0
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=dram 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --cpus-per-task=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=2:00:00 
<nowiki>#</nowiki>SBATCH --output=log.%j.out 
<nowiki>#</nowiki>SBATCH --error=log.%j.err 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 

cd $SLURM_SUBMIT_DIR 

ml DRAM-bio/1.4.0 

DRAM.py annotate -i <seq.fasta> -o outdir --threads <threads> 

</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml DRAM-bio/1.4.0
DRAM.py -h
usage: DRAM.py [-h] {annotate,annotate_genes,distill,strainer,neighborhoods,merge_annotations} ...

positional arguments:
{annotate,annotate_genes,distill,strainer,neighborhoods,merge_annotations}
annotate Annotate genomes/contigs/bins/MAGs
annotate_genes Annotate already called genes, limited functionality compared to annotate
distill Summarize metabolic content of annotated genomes
strainer Strain annotations down to genes of interest
neighborhoods Find neighborhoods around genes of interest
merge_annotations Merge multiple annotations to one larger set

options:
-h, --help show this help message and exit

DRAM.py annotate -h
usage: DRAM.py annotate [-h] -i INPUT_FASTA [-o OUTPUT_DIR] [--min_contig_size MIN_CONTIG_SIZE] [--prodigal_mode {train,meta,single}] [--trans_table {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25}] [--bit_score_threshold BIT_SCORE_THRESHOLD]
[--rbh_bit_score_threshold RBH_BIT_SCORE_THRESHOLD] [--kofam_use_dbcan2_thresholds] [--custom_db_name CUSTOM_DB_NAME] [--custom_fasta_loc CUSTOM_FASTA_LOC] [--custom_hmm_name CUSTOM_HMM_NAME] [--custom_hmm_loc CUSTOM_HMM_LOC]
[--custom_hmm_cutoffs_loc CUSTOM_HMM_CUTOFFS_LOC] [--gtdb_taxonomy GTDB_TAXONOMY] [--checkm_quality CHECKM_QUALITY] [--use_uniref] [--use_vogdb] [--low_mem_mode] [--skip_trnascan] [--keep_tmp_dir] [--threads THREADS] [--verbose]

options:
-h, --help show this help message and exit
-i INPUT_FASTA, --input_fasta INPUT_FASTA
fasta file, optionally with wildcards to point to multiple fastas (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
output directory (default: None)
--min_contig_size MIN_CONTIG_SIZE
minimum contig size to be used for gene prediction (default: 2500)
--prodigal_mode {train,meta,single}
Mode of prodigal to use for gene calling. NOTE: normal or single mode require genomes which are high quality with low contamination and long contigs (average length >3 Kbp). (default: meta)
--trans_table {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25}
Translation table for prodigal to use for gene calling. (default: 11)
--bit_score_threshold BIT_SCORE_THRESHOLD
minimum bitScore of search to retain hits (default: 60)
--rbh_bit_score_threshold RBH_BIT_SCORE_THRESHOLD
minimum bitScore of reverse best hits to retain hits (default: 350)
--kofam_use_dbcan2_thresholds
Use dbcan2 suggested HMM cutoffs for KOfam annotation instead of KOfam recommended cutoffs. This will be ignored if annotating with KEGG Genes. (default: False)
--custom_db_name CUSTOM_DB_NAME
Names of custom databases, can be usedmultiple times. (default: None)
--custom_fasta_loc CUSTOM_FASTA_LOC
Location of fastas to annotate against, can be used multiple times butmust match nubmer of custom_db_name's (default: [])
--custom_hmm_name CUSTOM_HMM_NAME
Names of custom hmm databases, can be used multiple times. (default: [])
--custom_hmm_loc CUSTOM_HMM_LOC
Location of hmms to annotate against, can be used multiple times butmust match nubmer of custom_hmm_name's (default: [])
--custom_hmm_cutoffs_loc CUSTOM_HMM_CUTOFFS_LOC
Location of file with custom HMM cutoffs and descriptions, can be used multiple times. (default: [])
--gtdb_taxonomy GTDB_TAXONOMY
Summary file from gtdbtk taxonomy assignment from bins, can be used multipletimes (default: [])
--checkm_quality CHECKM_QUALITY
Summary of of checkM quality assessment from bins, can be used multiple times (default: [])
--use_uniref Annotate these fastas against UniRef, drastically increases run time and memory requirements (default: False)
--use_vogdb Annotate these fastas against VOGDB, drastically decreases run time (default: False)
--low_mem_mode Skip annotating with uniref and use kofam instead of KEGG genes even if provided. Drastically decreases memory usage (default: False)
--skip_trnascan
--keep_tmp_dir
--threads THREADS number of processors to use (default: 10)
--verbose

DRAM.py annotate_genes -h
usage: DRAM.py annotate_genes [-h] -i INPUT_FAA [-o OUTPUT_DIR] [--bit_score_threshold BIT_SCORE_THRESHOLD] [--rbh_bit_score_threshold RBH_BIT_SCORE_THRESHOLD] [--kofam_use_dbcan2_thresholds] [--custom_db_name CUSTOM_DB_NAME] [--custom_fasta_loc CUSTOM_FASTA_LOC]
[--custom_hmm_name CUSTOM_HMM_NAME] [--custom_hmm_loc CUSTOM_HMM_LOC] [--custom_hmm_cutoffs_loc CUSTOM_HMM_CUTOFFS_LOC] [--use_uniref] [--low_mem_mode] [--keep_tmp_dir] [--threads THREADS] [--verbose]

options:
-h, --help show this help message and exit
-i INPUT_FAA, --input_faa INPUT_FAA
fasta file, optionally with wildcards to point to individual MAGs (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
output directory (default: None)
--bit_score_threshold BIT_SCORE_THRESHOLD
minimum bitScore of search to retain hits (default: 60)
--rbh_bit_score_threshold RBH_BIT_SCORE_THRESHOLD
minimum bitScore of reverse best hits to retain hits (default: 350)
--kofam_use_dbcan2_thresholds
Use dbcan2 suggested HMM cutoffs for KOfam annotation instead of KOfam recommended cutoffs. This will be ignored if annotating with KEGG Genes. (default: False)
--custom_db_name CUSTOM_DB_NAME
Names of custom databases, can be used multiple times. (default: [])
--custom_fasta_loc CUSTOM_FASTA_LOC
Location of fastas to annotate against, can be used multiple times butmust match nubmer of custom_db_name's (default: [])
--custom_hmm_name CUSTOM_HMM_NAME
Names of custom hmm databases, can be used multiple times. (default: [])
--custom_hmm_loc CUSTOM_HMM_LOC
Location of hmms to annotate against, can be used multiple times butmust match nubmer of custom_hmm_name's (default: [])
--custom_hmm_cutoffs_loc CUSTOM_HMM_CUTOFFS_LOC
Location of file with custom HMM cutoffs and descriptions, can be used multiple times. (default: [])
--use_uniref Annotate these fastas against UniRef, drastically increases run time and memory requirements (default: False)
--low_mem_mode Skip annotating with uniref and use kofam instead of KEGG genes even if provided. Drastically decreases memory usage (default: False)
--keep_tmp_dir
--threads THREADS number of processors to use (default: 10)
--verbose

DRAM.py distill -h
usage: DRAM.py distill [-h] [-i INPUT_FILE] [-o OUTPUT_DIR] [--rrna_path RRNA_PATH] [--trna_path TRNA_PATH] [--groupby_column GROUPBY_COLUMN] [--custom_distillate CUSTOM_DISTILLATE] [--distillate_gene_names] [--genomes_per_product GENOMES_PER_PRODUCT]

options:
-h, --help show this help message and exit
-i INPUT_FILE, --input_file INPUT_FILE
Annotations path (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
Directory to write summarized genomes (default: None)
--rrna_path RRNA_PATH
rRNA output from annotation (default: None)
--trna_path TRNA_PATH
tRNA output from annotation (default: None)
--groupby_column GROUPBY_COLUMN
Column from annotations to group as organism units (default: fasta)
--custom_distillate CUSTOM_DISTILLATE
Custom distillate form to add your own modules (default: None)
--distillate_gene_names
Give names of genes instead of counts in genome metabolism summary (default: False)
--genomes_per_product GENOMES_PER_PRODUCT
Number of genomes per product.html output. Decrease value if getting JavaScript Error: Maximum call stack size exceeded when viewing product.html in browser. (default: 1000)

DRAM.py strainer -h
usage: DRAM.py strainer [-h] -i INPUT_ANNOTATIONS -f INPUT_FASTA [-o OUTPUT_FASTA] [--fastas [FASTAS ...]] [--scaffolds [SCAFFOLDS ...]] [--genes [GENES ...]] [--identifiers [IDENTIFIERS ...]] [--categories [CATEGORIES ...]]
[--custom_distillate CUSTOM_DISTILLATE] [--taxonomy [TAXONOMY ...]] [--completeness COMPLETENESS] [--contamination CONTAMINATION]

options:
-h, --help show this help message and exit

Input and output files:
-i INPUT_ANNOTATIONS, --input_annotations INPUT_ANNOTATIONS
annotations file to pull genes from (default: None)
-f INPUT_FASTA, --input_fasta INPUT_FASTA
fasta file to filter (default: None)
-o OUTPUT_FASTA, --output_fasta OUTPUT_FASTA
location to write filtered fasta (default: pull_genes.fasta)

Specific names to keep:
--fastas [FASTAS ...]
space separated list of fastas to keep (default: None)
--scaffolds [SCAFFOLDS ...]
space separated list of scaffolds to keep (default: None)
--genes [GENES ...] space separated list of genes to keep (default: None)

Annotation filters:
--identifiers [IDENTIFIERS ...]
database identifiers to keep (default: None)
--categories [CATEGORIES ...]
distillate categories to keep genes from (default: None)
--custom_distillate CUSTOM_DISTILLATE
Custom distillate form to add your own modules (default: None)

DRAM based filters:
--taxonomy [TAXONOMY ...]
Level of GTDBTk taxonomy to keep (e.g. c__Clostridia), space separated list (default: None)
--completeness COMPLETENESS
Minimum completeness of genome to keep genes (default: None)
--contamination CONTAMINATION
Maximum contamination of genome to keep genes (default: None)

DRAM.py neighborhoods -h
usage: DRAM.py neighborhoods [-h] [-i INPUT_FILE] [-o OUTPUT_DIR] [--genes [GENES ...]] [--identifiers [IDENTIFIERS ...]] [--custom_distillate CUSTOM_DISTILLATE] [--categories CATEGORIES] [--genes_loc GENES_LOC] [--scaffolds_loc SCAFFOLDS_LOC]
[--distance_genes DISTANCE_GENES] [--distance_bp DISTANCE_BP]

options:
-h, --help show this help message and exit
-i INPUT_FILE, --input_file INPUT_FILE
Annotations path (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
Directory to write gene neighborhoods (default: None)
--genes [GENES ...] Gene names from DRAM to find neighborhoods around (default: None)
--identifiers [IDENTIFIERS ...]
Database identifiers assigned by DRAM to find neighborhoods around (default: None)
--custom_distillate CUSTOM_DISTILLATE
Custom distillate form to add your own modules (default: None)
--categories CATEGORIES
Distillate categories to build gene neighborhoods around. (default: None)
--genes_loc GENES_LOC
Location of genes.fna/genes.faa file to filter to neighborhoods (default: None)
--scaffolds_loc SCAFFOLDS_LOC
Location of scaffolds.fna file to filter to neighborhoods (default: None)
--distance_genes DISTANCE_GENES
Number of genes away from center to include in neighborhoods (default: None)
--distance_bp DISTANCE_BP
Number of genes away from center to include in neighborhoods (default: None)

DRAM.py merge_annotations -h
usage: DRAM.py merge_annotations [-h] [-i INPUT_DIRS] [-o OUTPUT_DIR]

options:
-h, --help show this help message and exit
-i INPUT_DIRS, --input_dirs INPUT_DIRS
Path with wildcards pointing to DRAM annotation output directories (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
Path to output merged annotations files (default: None)

DRAM-bio-Sapelo2

2022-11-07T17:29:23Z

Karen: Create page for DRAM-bio software

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
1.4.0

=== Author / Distributor ===

Please see https://github.com/WrightonLabCSU/DRAM

=== Description ===
DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs. DRAM annotates MAGs and viral contigs using KEGG (if provided by the user), UniRef90, PFAM, dbCAN, RefSeq viral, VOGDB and the MEROPS peptidase database as well as custom user databases.

The databases DRAM uses are already available on Sapelo2 in /db/DRAM_data/20222204/.

The database locations should be preset in the config file for DRAM-bio, you do not need to download them.

=== Running Program ===

* Version 1.4.0 is installed at /apps/eb/DRAM-bio/1.4.0/

To use version 1.4.0, please load the module with
<pre class="gscript">
ml DRAM-bio/1.4.0
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=dram 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --cpus-per-task=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=2:00:00 
<nowiki>#</nowiki>SBATCH --output=log.%j.out 
<nowiki>#</nowiki>SBATCH --error=log.%j.err 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 

cd $SLURM_SUBMIT_DIR 

ml DRAM-bio/1.4.0 

DRAM.py annotate -i <seq.fasta> -o outdir 

</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml DRAM-bio/1.4.0
DRAM.py -h
usage: DRAM.py [-h] {annotate,annotate_genes,distill,strainer,neighborhoods,merge_annotations} ...

positional arguments:
{annotate,annotate_genes,distill,strainer,neighborhoods,merge_annotations}
annotate Annotate genomes/contigs/bins/MAGs
annotate_genes Annotate already called genes, limited functionality compared to annotate
distill Summarize metabolic content of annotated genomes
strainer Strain annotations down to genes of interest
neighborhoods Find neighborhoods around genes of interest
merge_annotations Merge multiple annotations to one larger set

options:
-h, --help show this help message and exit

DRAM.py annotate -h
usage: DRAM.py annotate [-h] -i INPUT_FASTA [-o OUTPUT_DIR] [--min_contig_size MIN_CONTIG_SIZE] [--prodigal_mode {train,meta,single}] [--trans_table {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25}] [--bit_score_threshold BIT_SCORE_THRESHOLD]
[--rbh_bit_score_threshold RBH_BIT_SCORE_THRESHOLD] [--kofam_use_dbcan2_thresholds] [--custom_db_name CUSTOM_DB_NAME] [--custom_fasta_loc CUSTOM_FASTA_LOC] [--custom_hmm_name CUSTOM_HMM_NAME] [--custom_hmm_loc CUSTOM_HMM_LOC]
[--custom_hmm_cutoffs_loc CUSTOM_HMM_CUTOFFS_LOC] [--gtdb_taxonomy GTDB_TAXONOMY] [--checkm_quality CHECKM_QUALITY] [--use_uniref] [--use_vogdb] [--low_mem_mode] [--skip_trnascan] [--keep_tmp_dir] [--threads THREADS] [--verbose]

options:
-h, --help show this help message and exit
-i INPUT_FASTA, --input_fasta INPUT_FASTA
fasta file, optionally with wildcards to point to multiple fastas (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
output directory (default: None)
--min_contig_size MIN_CONTIG_SIZE
minimum contig size to be used for gene prediction (default: 2500)
--prodigal_mode {train,meta,single}
Mode of prodigal to use for gene calling. NOTE: normal or single mode require genomes which are high quality with low contamination and long contigs (average length >3 Kbp). (default: meta)
--trans_table {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25}
Translation table for prodigal to use for gene calling. (default: 11)
--bit_score_threshold BIT_SCORE_THRESHOLD
minimum bitScore of search to retain hits (default: 60)
--rbh_bit_score_threshold RBH_BIT_SCORE_THRESHOLD
minimum bitScore of reverse best hits to retain hits (default: 350)
--kofam_use_dbcan2_thresholds
Use dbcan2 suggested HMM cutoffs for KOfam annotation instead of KOfam recommended cutoffs. This will be ignored if annotating with KEGG Genes. (default: False)
--custom_db_name CUSTOM_DB_NAME
Names of custom databases, can be usedmultiple times. (default: None)
--custom_fasta_loc CUSTOM_FASTA_LOC
Location of fastas to annotate against, can be used multiple times butmust match nubmer of custom_db_name's (default: [])
--custom_hmm_name CUSTOM_HMM_NAME
Names of custom hmm databases, can be used multiple times. (default: [])
--custom_hmm_loc CUSTOM_HMM_LOC
Location of hmms to annotate against, can be used multiple times butmust match nubmer of custom_hmm_name's (default: [])
--custom_hmm_cutoffs_loc CUSTOM_HMM_CUTOFFS_LOC
Location of file with custom HMM cutoffs and descriptions, can be used multiple times. (default: [])
--gtdb_taxonomy GTDB_TAXONOMY
Summary file from gtdbtk taxonomy assignment from bins, can be used multipletimes (default: [])
--checkm_quality CHECKM_QUALITY
Summary of of checkM quality assessment from bins, can be used multiple times (default: [])
--use_uniref Annotate these fastas against UniRef, drastically increases run time and memory requirements (default: False)
--use_vogdb Annotate these fastas against VOGDB, drastically decreases run time (default: False)
--low_mem_mode Skip annotating with uniref and use kofam instead of KEGG genes even if provided. Drastically decreases memory usage (default: False)
--skip_trnascan
--keep_tmp_dir
--threads THREADS number of processors to use (default: 10)
--verbose

DRAM.py annotate_genes -h
usage: DRAM.py annotate_genes [-h] -i INPUT_FAA [-o OUTPUT_DIR] [--bit_score_threshold BIT_SCORE_THRESHOLD] [--rbh_bit_score_threshold RBH_BIT_SCORE_THRESHOLD] [--kofam_use_dbcan2_thresholds] [--custom_db_name CUSTOM_DB_NAME] [--custom_fasta_loc CUSTOM_FASTA_LOC]
[--custom_hmm_name CUSTOM_HMM_NAME] [--custom_hmm_loc CUSTOM_HMM_LOC] [--custom_hmm_cutoffs_loc CUSTOM_HMM_CUTOFFS_LOC] [--use_uniref] [--low_mem_mode] [--keep_tmp_dir] [--threads THREADS] [--verbose]

options:
-h, --help show this help message and exit
-i INPUT_FAA, --input_faa INPUT_FAA
fasta file, optionally with wildcards to point to individual MAGs (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
output directory (default: None)
--bit_score_threshold BIT_SCORE_THRESHOLD
minimum bitScore of search to retain hits (default: 60)
--rbh_bit_score_threshold RBH_BIT_SCORE_THRESHOLD
minimum bitScore of reverse best hits to retain hits (default: 350)
--kofam_use_dbcan2_thresholds
Use dbcan2 suggested HMM cutoffs for KOfam annotation instead of KOfam recommended cutoffs. This will be ignored if annotating with KEGG Genes. (default: False)
--custom_db_name CUSTOM_DB_NAME
Names of custom databases, can be used multiple times. (default: [])
--custom_fasta_loc CUSTOM_FASTA_LOC
Location of fastas to annotate against, can be used multiple times butmust match nubmer of custom_db_name's (default: [])
--custom_hmm_name CUSTOM_HMM_NAME
Names of custom hmm databases, can be used multiple times. (default: [])
--custom_hmm_loc CUSTOM_HMM_LOC
Location of hmms to annotate against, can be used multiple times butmust match nubmer of custom_hmm_name's (default: [])
--custom_hmm_cutoffs_loc CUSTOM_HMM_CUTOFFS_LOC
Location of file with custom HMM cutoffs and descriptions, can be used multiple times. (default: [])
--use_uniref Annotate these fastas against UniRef, drastically increases run time and memory requirements (default: False)
--low_mem_mode Skip annotating with uniref and use kofam instead of KEGG genes even if provided. Drastically decreases memory usage (default: False)
--keep_tmp_dir
--threads THREADS number of processors to use (default: 10)
--verbose

DRAM.py distill -h
usage: DRAM.py distill [-h] [-i INPUT_FILE] [-o OUTPUT_DIR] [--rrna_path RRNA_PATH] [--trna_path TRNA_PATH] [--groupby_column GROUPBY_COLUMN] [--custom_distillate CUSTOM_DISTILLATE] [--distillate_gene_names] [--genomes_per_product GENOMES_PER_PRODUCT]

options:
-h, --help show this help message and exit
-i INPUT_FILE, --input_file INPUT_FILE
Annotations path (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
Directory to write summarized genomes (default: None)
--rrna_path RRNA_PATH
rRNA output from annotation (default: None)
--trna_path TRNA_PATH
tRNA output from annotation (default: None)
--groupby_column GROUPBY_COLUMN
Column from annotations to group as organism units (default: fasta)
--custom_distillate CUSTOM_DISTILLATE
Custom distillate form to add your own modules (default: None)
--distillate_gene_names
Give names of genes instead of counts in genome metabolism summary (default: False)
--genomes_per_product GENOMES_PER_PRODUCT
Number of genomes per product.html output. Decrease value if getting JavaScript Error: Maximum call stack size exceeded when viewing product.html in browser. (default: 1000)

DRAM.py strainer -h
usage: DRAM.py strainer [-h] -i INPUT_ANNOTATIONS -f INPUT_FASTA [-o OUTPUT_FASTA] [--fastas [FASTAS ...]] [--scaffolds [SCAFFOLDS ...]] [--genes [GENES ...]] [--identifiers [IDENTIFIERS ...]] [--categories [CATEGORIES ...]]
[--custom_distillate CUSTOM_DISTILLATE] [--taxonomy [TAXONOMY ...]] [--completeness COMPLETENESS] [--contamination CONTAMINATION]

options:
-h, --help show this help message and exit

Input and output files:
-i INPUT_ANNOTATIONS, --input_annotations INPUT_ANNOTATIONS
annotations file to pull genes from (default: None)
-f INPUT_FASTA, --input_fasta INPUT_FASTA
fasta file to filter (default: None)
-o OUTPUT_FASTA, --output_fasta OUTPUT_FASTA
location to write filtered fasta (default: pull_genes.fasta)

Specific names to keep:
--fastas [FASTAS ...]
space separated list of fastas to keep (default: None)
--scaffolds [SCAFFOLDS ...]
space separated list of scaffolds to keep (default: None)
--genes [GENES ...] space separated list of genes to keep (default: None)

Annotation filters:
--identifiers [IDENTIFIERS ...]
database identifiers to keep (default: None)
--categories [CATEGORIES ...]
distillate categories to keep genes from (default: None)
--custom_distillate CUSTOM_DISTILLATE
Custom distillate form to add your own modules (default: None)

DRAM based filters:
--taxonomy [TAXONOMY ...]
Level of GTDBTk taxonomy to keep (e.g. c__Clostridia), space separated list (default: None)
--completeness COMPLETENESS
Minimum completeness of genome to keep genes (default: None)
--contamination CONTAMINATION
Maximum contamination of genome to keep genes (default: None)

DRAM.py neighborhoods -h
usage: DRAM.py neighborhoods [-h] [-i INPUT_FILE] [-o OUTPUT_DIR] [--genes [GENES ...]] [--identifiers [IDENTIFIERS ...]] [--custom_distillate CUSTOM_DISTILLATE] [--categories CATEGORIES] [--genes_loc GENES_LOC] [--scaffolds_loc SCAFFOLDS_LOC]
[--distance_genes DISTANCE_GENES] [--distance_bp DISTANCE_BP]

options:
-h, --help show this help message and exit
-i INPUT_FILE, --input_file INPUT_FILE
Annotations path (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
Directory to write gene neighborhoods (default: None)
--genes [GENES ...] Gene names from DRAM to find neighborhoods around (default: None)
--identifiers [IDENTIFIERS ...]
Database identifiers assigned by DRAM to find neighborhoods around (default: None)
--custom_distillate CUSTOM_DISTILLATE
Custom distillate form to add your own modules (default: None)
--categories CATEGORIES
Distillate categories to build gene neighborhoods around. (default: None)
--genes_loc GENES_LOC
Location of genes.fna/genes.faa file to filter to neighborhoods (default: None)
--scaffolds_loc SCAFFOLDS_LOC
Location of scaffolds.fna file to filter to neighborhoods (default: None)
--distance_genes DISTANCE_GENES
Number of genes away from center to include in neighborhoods (default: None)
--distance_bp DISTANCE_BP
Number of genes away from center to include in neighborhoods (default: None)

DRAM.py merge_annotations -h
usage: DRAM.py merge_annotations [-h] [-i INPUT_DIRS] [-o OUTPUT_DIR]

options:
-h, --help show this help message and exit
-i INPUT_DIRS, --input_dirs INPUT_DIRS
Path with wildcards pointing to DRAM annotation output directories (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
Path to output merged annotations files (default: None)

Software

2022-11-07T17:10:24Z

Karen: /* Partial List of Installed Software */

,On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 600 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold]] || 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.2.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 18, 22 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
















| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.2, 2.6.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[BionanoSolve-Sapelo2|BionanoSolve]] || 3.6.1-11162020 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



|[[Biopython-Teaching|Biopython]] || 1.75 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.2.31, 2.9.0, 2.10.1,2.11.0,2.12.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.9.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[BLAST-Teaching|BLAST]] || 2.2.26 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Bowtie2-Teaching|Bowtie2]] || 2.3.5.1, 2.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[BUSCO-Sapelo2|BUSCO]] || 4.0.5, 4.0.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Canu-Sapelo2|Canu]] || 2.1.1|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 1.2.0, 2.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
































| [[cryoSPARC-Sapelo2|cryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
|[[CUDA-Sapelo2|CUDA]] || 9.2.88, 10.1.243, 11.0.2, 11.1.1, 11.2.1 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Cytoscape-Teaching|Cytoscape]] || 3.7.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|
|-


























| [[DRAM-bio-Sapelo2|DRAM-bio]] || 1.4.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




















































| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.0, 1.1, 1.2, 1.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMarkES]] || 4.57 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


































| [[GROMACS-Sapelo2 |GROMACS]] || 4.5.6,2019.4,2020,2020.3,2021.2,2021.3,2021.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



















| [[HISAT2-Teaching|HISAT2]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.44-90.0, 5.51-85.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




| [[IQ-Tree-Teaching|IQ-Tree]] || 1.6.12|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_144, 1.8.0_241, 11.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 5.0.0, 5.6.0, 6.0.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 3Mar2020 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.25 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.03 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2019b, R2020a, R2020b, R2021a, R2021b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































| [[MOTECC_qmdcp-Teaching|MOTECC_qmdcp]] || 90 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Mothur-Sapelo2|Mothur]] || 1.39.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[MrBayes-Sapelo2|MrBayes]] || 3.2.6, 3.2.7a || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


















































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 4.4.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




|[[ORP-Sapelo2|ORP]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.3.8, 2.3.11, 2.5.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[OrthoMCL-Sapelo2|OrthoMCL]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[PAML-Teaching|PAML]] || 4.9i || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->























| [[Perl-Teaching|Perl]] || 5.30.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.19.2-4158 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Pong-Sapelo2|Pong]] || 1.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.14, 2.7.15, 2.7.16, 3.7.4, 3.8.2, 3.8.6, 3.9.5 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 3.7.4, 2.7.16 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2019.10, 2020.2, 2020.6, 2020.11 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 3.5.0, 3.6.2, 4.0.0, 4.1.0, 4.1.3, 4.2.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.0.0 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.4.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[RAxML-Sapelo2 |RAxML]] || 8.2.11, 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2020.28.61328, 2021.16.61629 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 1.1.463, 1.2.5033, 1.4.1103, 2022.02.1-461, 2022.07.1-554 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.9, 1.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->































| [[smoke-Sapelo2|smoke]] || 4.7 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

































| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 2.9.6-1,2.10.8,2.11.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.9.1, 2.10.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

Software

2022-11-07T17:01:02Z

Karen: add dram to list

,On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 600 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold]] || 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.2.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 18, 22 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
















| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.2, 2.6.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[BionanoSolve-Sapelo2|BionanoSolve]] || 3.6.1-11162020 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



|[[Biopython-Teaching|Biopython]] || 1.75 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.2.31, 2.9.0, 2.10.1,2.11.0,2.12.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.9.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[BLAST-Teaching|BLAST]] || 2.2.26 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Bowtie2-Teaching|Bowtie2]] || 2.3.5.1, 2.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[BUSCO-Sapelo2|BUSCO]] || 4.0.5, 4.0.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Canu-Sapelo2|Canu]] || 2.1.1|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 1.2.0, 2.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
































| [[cryoSPARC-Sapelo2|cryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
|[[CUDA-Sapelo2|CUDA]] || 9.2.88, 10.1.243, 11.0.2, 11.1.1, 11.2.1 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Cytoscape-Teaching|Cytoscape]] || 3.7.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




















































| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.0, 1.1, 1.2, 1.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMarkES]] || 4.57 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


































| [[GROMACS-Sapelo2 |GROMACS]] || 4.5.6,2019.4,2020,2020.3,2021.2,2021.3,2021.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



















| [[HISAT2-Teaching|HISAT2]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.44-90.0, 5.51-85.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




| [[IQ-Tree-Teaching|IQ-Tree]] || 1.6.12|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_144, 1.8.0_241, 11.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 5.0.0, 5.6.0, 6.0.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 3Mar2020 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.25 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.03 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2019b, R2020a, R2020b, R2021a, R2021b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































| [[MOTECC_qmdcp-Teaching|MOTECC_qmdcp]] || 90 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Mothur-Sapelo2|Mothur]] || 1.39.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[MrBayes-Sapelo2|MrBayes]] || 3.2.6, 3.2.7a || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


















































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 4.4.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




|[[ORP-Sapelo2|ORP]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.3.8, 2.3.11, 2.5.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[OrthoMCL-Sapelo2|OrthoMCL]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[PAML-Teaching|PAML]] || 4.9i || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->























| [[Perl-Teaching|Perl]] || 5.30.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.19.2-4158 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Pong-Sapelo2|Pong]] || 1.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.14, 2.7.15, 2.7.16, 3.7.4, 3.8.2, 3.8.6, 3.9.5 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 3.7.4, 2.7.16 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2019.10, 2020.2, 2020.6, 2020.11 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 3.5.0, 3.6.2, 4.0.0, 4.1.0, 4.1.3, 4.2.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.0.0 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.4.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[RAxML-Sapelo2 |RAxML]] || 8.2.11, 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2020.28.61328, 2021.16.61629 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 1.1.463, 1.2.5033, 1.4.1103, 2022.02.1-461, 2022.07.1-554 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.9, 1.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->































| [[smoke-Sapelo2|smoke]] || 4.7 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

































| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 2.9.6-1,2.10.8,2.11.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.9.1, 2.10.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

UBCG-Sapelo2

2022-11-02T20:29:37Z

Karen: /* Running Program */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
3.0

=== Author / Distributor ===

Please see https://www.ezbiocloud.net/tools/ubcg

=== Description ===
The 16S rRNA gene has played an essential role in bacterial taxonomy by providing a universally applicable phylogenetic framework. However, this single gene contains only about 1,500 bp which inheritably limits the resolution of the analysis. Here, we present the set of bacterial core genes that covers all phyla, which we named UBCG (up-to-date bacterial core gene). The current UBCG set was calculated using complete genomes of 1,492 species covering 28 phyla, consisting of 92 genes.

The package provides the following features:
Extraction of UBCGs from genome assemblies
Multiple-alignment of 92 gene sequences
Concatenation of 92 gene sequences
Filtering positions of multiple-alignments
Phylogenetic analysis using RAxML and FastTree
Calculation of Gene Support Index (GSI) which indicates how many genes support the branch in the concatenated phylogenetic tree (named UBCG tree)
=== Running Program ===

* Version 3.0 is installed at /apps/eb/UBCG/3.0-foss-2019b-Java-1.8.0_144

To use version 3.0, please load the module with
<pre class="gscript">
ml UBCG/3.0-foss-2019b-Java-1.8.0_144
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=ubcg 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --cpus-per-task=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=2:00:00 
<nowiki>#</nowiki>SBATCH --output=log.%j.out 
<nowiki>#</nowiki>SBATCH --error=log.%j.err 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 

cd $SLURM_SUBMIT_DIR 
ml UBCG/3.0-foss-2019b-Java-1.8.0_144 

<nowiki>#</nowiki>copy these two files to your working directory for UBCG to run properly

cp $EBROOTUBCG/UBCG.hmm ./ 
cp $EBROOTUBCG/programPath ./ 

java -jar $EBROOTUBCG/UBCG.jar extract -i <sequence_file>.fa -bcg_dir <output_directory> -label "<Genus species>" 

</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml UBCG/3.0-foss-2019b-Java-1.8.0_144
java -jar $EBROOTUBCG/UBCG.jar --help

###############################
# UBCG ver. 3.0 #
###############################

UBCG is a program for phylogenetic analysis using the single-copy bacterial core genes

The external programs that are used in the UBCG should be installed
The locations of programs should be written in 'programPath' file

Basic options
-h : Show usage and options (--help)

---- Running phylogenetic analysis workflow through two-step command ----

<Step 1>
Searching UBCGs from a genome sequence

java -jar UBCG.jar extract [-i genome_file] [-bcg_dir bcg_directory] [-label full_label]

Mandatory arguments
-i <String> : Name of input fasta file containing contigs
-bcg_dir <String> : Directory for saving a bcg file
-label <String> : Full label of the strain/genome

Optional arguments
-g <Integer> : A translation table to be used for translation (-g parameter used in Prodigal)
Use this option when you enter a genome of species which uses other genetic code
Most of the bacteria uses the 11 table
(Default : 11, the bacterial and archaeal code)
-t <Integer> : Number of threads to be used
(Default : 8)

Metadata of input genome(Optional)
-taxon <String> : Name of the species
-strain <String> : Name of the strain
-type : Add this if the strain is a type strain of species or subspecies
-acc <String> : Accession of genome sequence. Usually NCBI's assembly accession is used for public data
-uid <Integer> : This is a unique integer id. If you do not designate, one will be automatically generated
-taxonomy <String> : Taxonomy of the species

<Step 2>
Aligning each UBCG and concatenating them and inferring a phylogeny
The external program used for phylogeny reconstruction can be FastTree or RAxML

java -jar UBCG.jar align [-bcg_dir bcg_directory]

Mandatory arguments
-bcg_dir <String> : Directory of bcg files that you want to include in the alignment

Optional arguments
-out_dir <String> : Directory where all output files will be
(Default : "output")
-prefix <String> : A prefix is appended to all output files to recognize each different run
-a <String> : Type of sequences to be aligned and used for the phylogenetic analysis
(Default : codon)
Enter one among the below options
nt : Use nucleotide sequences
codon : Use nucleotide sequences that are aligned based on amino acid alignments
codon12 : Use only 1st & 2nd positions of codon
aa : Use amino acid sequences
-m <String> : A model used to infer trees
(Default : JTT+CAT for a protein alignment / GTR+CAT for a nucleotide alignment)
--Models (See RAxML or FastTree manual for the detailed information)
For RAxML - NUCLEOTIDE sequences
GTRCAT[X], GTRCATI[X], ASC_GTRCAT[X],
GTRGAMMA[X], ASC_GTRGAMMA[X], GTRGAMMAI[X]
- AMINO ACID sequences
PROTCATmatrixName[F|X], PROTCATImatrixName[F|X],
ASC_PROTCATmatrixName[F|X], PROTGAMMAmatrixName[F|X],
ASC_PROTGAMMAmatrixName[F|X], PROTGAMMAImatrixName[F|X]
Available aa matrixName: DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT,
BLOSUM62, MTMAM, LG, MTART, MTZOA, PMB, HIVB, HIVW,
JTTDCMUT, FLU, STMTREV, DUMMY, DUMMY2, AUTO, LG4M,
LG4X, PROT_FILE, GTR_UNLINKED, GTR
(optional appendix "F": Use empirical base frequencies)
(optional appendix "X": Use a ML estimate of base frequencies)
For FastTree - NUCLEOTIDE sequences
JCcat, GTRcat, JCgamma, GTRgamma
- AMINO ACID sequences
JTTcat, LGcat, WAGcat, JTTgamma, LGgamma, WAGgamma
-t <Integer> : Number of threads to be used
(Default : 1)
-f <Value> : Filter gap-containing positions
Enter a value between 1~100
(Default: 50)
ex) 30 : select the positions that have bases of 30% or more
(remove the positions composed of more than 70% gap characters)
-raxml : Use RAxML for phylogeny reconstruction
(Default: FastTree)
-zZ : Make zZ-formatted files
This additionally creates fasta/nwk files with zZ'uid'zZ format for names of each genome
-gsi_threshold: The threshold used for GSI calculations (1~100)
Even if the exact bipartition doesn't exist in a gene tree, it is regarded as a supported bipartition based on their similiarity
It is when the number of genomes more than specified threshold(percentage) of all genomes(leaves) support the topology of bipartition
A value of 95 or higher is recommended
(Default: 95)

---- Replacing labels -----
Replacing labels in a tree using metadata

java -jar UBCG.jar replace <run_id..trm> <gene>
ex) java -jar UBCG.jar replace 'run_id'.trm UBCG -taxon -strain
Making a UBCG tree file that uses both taxon_name and strain_name as labels
ex) java -jar UBCG.jar replace 'run_id'.trm rpoB -acc -taxon -type
Making a rpoB tree file that uses accession, taxon_name and strain_name as labels

Parameters
<run_id.trm> : A file containing trees with metadata. This file is automatically generated in the step 2
<gene> : The gene trees or UBCG tree you want to replace
-uid : add uids
-acc : add accessions
-label : add labels
-taxon : add taxon_names
-strain : add strain_names
-type : add type_info
-taxonomy : add taxonomy

---- Showing the content of bcg files ----
The content of bcg files (for example, gene sequences) can be viewed (as csv format that is readable by Microsoft Excel) by using the following command:

java -jar UBCG.jar view -i <a bcg file>
java -jar UBCG.jar view -d <directory containing bcg files>

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is download from https://www.ezbiocloud.net/tools/ubcg

=== System ===
64-bit Linux

UBCG-Sapelo2

2022-11-02T20:27:30Z

Karen: /* Running Program */

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
3.0

=== Author / Distributor ===

Please see https://www.ezbiocloud.net/tools/ubcg

=== Description ===
The 16S rRNA gene has played an essential role in bacterial taxonomy by providing a universally applicable phylogenetic framework. However, this single gene contains only about 1,500 bp which inheritably limits the resolution of the analysis. Here, we present the set of bacterial core genes that covers all phyla, which we named UBCG (up-to-date bacterial core gene). The current UBCG set was calculated using complete genomes of 1,492 species covering 28 phyla, consisting of 92 genes.

The package provides the following features:
Extraction of UBCGs from genome assemblies
Multiple-alignment of 92 gene sequences
Concatenation of 92 gene sequences
Filtering positions of multiple-alignments
Phylogenetic analysis using RAxML and FastTree
Calculation of Gene Support Index (GSI) which indicates how many genes support the branch in the concatenated phylogenetic tree (named UBCG tree)
=== Running Program ===

* Version 3.0 is installed at /apps/eb/UBCG/3.0-foss-2019b-Java-1.8.0_144

To use version 3.0, please load the module with
<pre class="gscript">
ml UBCG/3.0-foss-2019b-Java-1.8.0_144
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=ubcg 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --cpus-per-task=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=2:00:00 
<nowiki>#</nowiki>SBATCH --output=log.%j.out 
<nowiki>#</nowiki>SBATCH --error=log.%j.err 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 

cd $SLURM_SUBMIT_DIR 
ml UBCG/3.0-foss-2019b-Java-1.8.0_144 

cp $EBROOTUBCG/UBCG.hmm ./ 
cp $EBROOTUBCG/programPath ./ 

java -jar $EBROOTUBCG/UBCG.jar extract -i <sequence_file>.fa -bcg_dir <output_directory> -label "<Genus species>" 

</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml UBCG/3.0-foss-2019b-Java-1.8.0_144
java -jar $EBROOTUBCG/UBCG.jar --help

###############################
# UBCG ver. 3.0 #
###############################

UBCG is a program for phylogenetic analysis using the single-copy bacterial core genes

The external programs that are used in the UBCG should be installed
The locations of programs should be written in 'programPath' file

Basic options
-h : Show usage and options (--help)

---- Running phylogenetic analysis workflow through two-step command ----

<Step 1>
Searching UBCGs from a genome sequence

java -jar UBCG.jar extract [-i genome_file] [-bcg_dir bcg_directory] [-label full_label]

Mandatory arguments
-i <String> : Name of input fasta file containing contigs
-bcg_dir <String> : Directory for saving a bcg file
-label <String> : Full label of the strain/genome

Optional arguments
-g <Integer> : A translation table to be used for translation (-g parameter used in Prodigal)
Use this option when you enter a genome of species which uses other genetic code
Most of the bacteria uses the 11 table
(Default : 11, the bacterial and archaeal code)
-t <Integer> : Number of threads to be used
(Default : 8)

Metadata of input genome(Optional)
-taxon <String> : Name of the species
-strain <String> : Name of the strain
-type : Add this if the strain is a type strain of species or subspecies
-acc <String> : Accession of genome sequence. Usually NCBI's assembly accession is used for public data
-uid <Integer> : This is a unique integer id. If you do not designate, one will be automatically generated
-taxonomy <String> : Taxonomy of the species

<Step 2>
Aligning each UBCG and concatenating them and inferring a phylogeny
The external program used for phylogeny reconstruction can be FastTree or RAxML

java -jar UBCG.jar align [-bcg_dir bcg_directory]

Mandatory arguments
-bcg_dir <String> : Directory of bcg files that you want to include in the alignment

Optional arguments
-out_dir <String> : Directory where all output files will be
(Default : "output")
-prefix <String> : A prefix is appended to all output files to recognize each different run
-a <String> : Type of sequences to be aligned and used for the phylogenetic analysis
(Default : codon)
Enter one among the below options
nt : Use nucleotide sequences
codon : Use nucleotide sequences that are aligned based on amino acid alignments
codon12 : Use only 1st & 2nd positions of codon
aa : Use amino acid sequences
-m <String> : A model used to infer trees
(Default : JTT+CAT for a protein alignment / GTR+CAT for a nucleotide alignment)
--Models (See RAxML or FastTree manual for the detailed information)
For RAxML - NUCLEOTIDE sequences
GTRCAT[X], GTRCATI[X], ASC_GTRCAT[X],
GTRGAMMA[X], ASC_GTRGAMMA[X], GTRGAMMAI[X]
- AMINO ACID sequences
PROTCATmatrixName[F|X], PROTCATImatrixName[F|X],
ASC_PROTCATmatrixName[F|X], PROTGAMMAmatrixName[F|X],
ASC_PROTGAMMAmatrixName[F|X], PROTGAMMAImatrixName[F|X]
Available aa matrixName: DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT,
BLOSUM62, MTMAM, LG, MTART, MTZOA, PMB, HIVB, HIVW,
JTTDCMUT, FLU, STMTREV, DUMMY, DUMMY2, AUTO, LG4M,
LG4X, PROT_FILE, GTR_UNLINKED, GTR
(optional appendix "F": Use empirical base frequencies)
(optional appendix "X": Use a ML estimate of base frequencies)
For FastTree - NUCLEOTIDE sequences
JCcat, GTRcat, JCgamma, GTRgamma
- AMINO ACID sequences
JTTcat, LGcat, WAGcat, JTTgamma, LGgamma, WAGgamma
-t <Integer> : Number of threads to be used
(Default : 1)
-f <Value> : Filter gap-containing positions
Enter a value between 1~100
(Default: 50)
ex) 30 : select the positions that have bases of 30% or more
(remove the positions composed of more than 70% gap characters)
-raxml : Use RAxML for phylogeny reconstruction
(Default: FastTree)
-zZ : Make zZ-formatted files
This additionally creates fasta/nwk files with zZ'uid'zZ format for names of each genome
-gsi_threshold: The threshold used for GSI calculations (1~100)
Even if the exact bipartition doesn't exist in a gene tree, it is regarded as a supported bipartition based on their similiarity
It is when the number of genomes more than specified threshold(percentage) of all genomes(leaves) support the topology of bipartition
A value of 95 or higher is recommended
(Default: 95)

---- Replacing labels -----
Replacing labels in a tree using metadata

java -jar UBCG.jar replace <run_id..trm> <gene>
ex) java -jar UBCG.jar replace 'run_id'.trm UBCG -taxon -strain
Making a UBCG tree file that uses both taxon_name and strain_name as labels
ex) java -jar UBCG.jar replace 'run_id'.trm rpoB -acc -taxon -type
Making a rpoB tree file that uses accession, taxon_name and strain_name as labels

Parameters
<run_id.trm> : A file containing trees with metadata. This file is automatically generated in the step 2
<gene> : The gene trees or UBCG tree you want to replace
-uid : add uids
-acc : add accessions
-label : add labels
-taxon : add taxon_names
-strain : add strain_names
-type : add type_info
-taxonomy : add taxonomy

---- Showing the content of bcg files ----
The content of bcg files (for example, gene sequences) can be viewed (as csv format that is readable by Microsoft Excel) by using the following command:

java -jar UBCG.jar view -i <a bcg file>
java -jar UBCG.jar view -d <directory containing bcg files>

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is download from https://www.ezbiocloud.net/tools/ubcg

=== System ===
64-bit Linux

UBCG-Sapelo2

2022-11-02T20:26:38Z

Karen: Create UBCG software page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
3.0

=== Author / Distributor ===

Please see https://www.ezbiocloud.net/tools/ubcg

=== Description ===
The 16S rRNA gene has played an essential role in bacterial taxonomy by providing a universally applicable phylogenetic framework. However, this single gene contains only about 1,500 bp which inheritably limits the resolution of the analysis. Here, we present the set of bacterial core genes that covers all phyla, which we named UBCG (up-to-date bacterial core gene). The current UBCG set was calculated using complete genomes of 1,492 species covering 28 phyla, consisting of 92 genes.

The package provides the following features:
Extraction of UBCGs from genome assemblies
Multiple-alignment of 92 gene sequences
Concatenation of 92 gene sequences
Filtering positions of multiple-alignments
Phylogenetic analysis using RAxML and FastTree
Calculation of Gene Support Index (GSI) which indicates how many genes support the branch in the concatenated phylogenetic tree (named UBCG tree)
=== Running Program ===

* Version 3.0 is installed at /apps/eb/UBCG/3.0-foss-2019b-Java-1.8.0_144

To use version 3.0, please load the module with
<pre class="gscript">
ml UBCG/3.0-foss-2019b-Java-1.8.0_144
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=ubcg 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --cpus-per-task=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=2:00:00 
<nowiki>#</nowiki>SBATCH --output=log.%j.out 
<nowiki>#</nowiki>SBATCH --error=log.%j.err 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 

cd $SLURM_SUBMIT_DIR 
ml UBCG/3.0-foss-2019b-Java-1.8.0_144 

cp $EBROOTUBCG/UBCG.hmm ./ 
cp $EBROOTUBCG/programPath ./ 

java -jar $EBROOTUBCG/UBCG.jar extract -i <sequence_file>.fa -bcg_dir <output_directory> -label "<Genus Species>" 

</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml UBCG/3.0-foss-2019b-Java-1.8.0_144
java -jar $EBROOTUBCG/UBCG.jar --help

###############################
# UBCG ver. 3.0 #
###############################

UBCG is a program for phylogenetic analysis using the single-copy bacterial core genes

The external programs that are used in the UBCG should be installed
The locations of programs should be written in 'programPath' file

Basic options
-h : Show usage and options (--help)

---- Running phylogenetic analysis workflow through two-step command ----

<Step 1>
Searching UBCGs from a genome sequence

java -jar UBCG.jar extract [-i genome_file] [-bcg_dir bcg_directory] [-label full_label]

Mandatory arguments
-i <String> : Name of input fasta file containing contigs
-bcg_dir <String> : Directory for saving a bcg file
-label <String> : Full label of the strain/genome

Optional arguments
-g <Integer> : A translation table to be used for translation (-g parameter used in Prodigal)
Use this option when you enter a genome of species which uses other genetic code
Most of the bacteria uses the 11 table
(Default : 11, the bacterial and archaeal code)
-t <Integer> : Number of threads to be used
(Default : 8)

Metadata of input genome(Optional)
-taxon <String> : Name of the species
-strain <String> : Name of the strain
-type : Add this if the strain is a type strain of species or subspecies
-acc <String> : Accession of genome sequence. Usually NCBI's assembly accession is used for public data
-uid <Integer> : This is a unique integer id. If you do not designate, one will be automatically generated
-taxonomy <String> : Taxonomy of the species

<Step 2>
Aligning each UBCG and concatenating them and inferring a phylogeny
The external program used for phylogeny reconstruction can be FastTree or RAxML

java -jar UBCG.jar align [-bcg_dir bcg_directory]

Mandatory arguments
-bcg_dir <String> : Directory of bcg files that you want to include in the alignment

Optional arguments
-out_dir <String> : Directory where all output files will be
(Default : "output")
-prefix <String> : A prefix is appended to all output files to recognize each different run
-a <String> : Type of sequences to be aligned and used for the phylogenetic analysis
(Default : codon)
Enter one among the below options
nt : Use nucleotide sequences
codon : Use nucleotide sequences that are aligned based on amino acid alignments
codon12 : Use only 1st & 2nd positions of codon
aa : Use amino acid sequences
-m <String> : A model used to infer trees
(Default : JTT+CAT for a protein alignment / GTR+CAT for a nucleotide alignment)
--Models (See RAxML or FastTree manual for the detailed information)
For RAxML - NUCLEOTIDE sequences
GTRCAT[X], GTRCATI[X], ASC_GTRCAT[X],
GTRGAMMA[X], ASC_GTRGAMMA[X], GTRGAMMAI[X]
- AMINO ACID sequences
PROTCATmatrixName[F|X], PROTCATImatrixName[F|X],
ASC_PROTCATmatrixName[F|X], PROTGAMMAmatrixName[F|X],
ASC_PROTGAMMAmatrixName[F|X], PROTGAMMAImatrixName[F|X]
Available aa matrixName: DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT,
BLOSUM62, MTMAM, LG, MTART, MTZOA, PMB, HIVB, HIVW,
JTTDCMUT, FLU, STMTREV, DUMMY, DUMMY2, AUTO, LG4M,
LG4X, PROT_FILE, GTR_UNLINKED, GTR
(optional appendix "F": Use empirical base frequencies)
(optional appendix "X": Use a ML estimate of base frequencies)
For FastTree - NUCLEOTIDE sequences
JCcat, GTRcat, JCgamma, GTRgamma
- AMINO ACID sequences
JTTcat, LGcat, WAGcat, JTTgamma, LGgamma, WAGgamma
-t <Integer> : Number of threads to be used
(Default : 1)
-f <Value> : Filter gap-containing positions
Enter a value between 1~100
(Default: 50)
ex) 30 : select the positions that have bases of 30% or more
(remove the positions composed of more than 70% gap characters)
-raxml : Use RAxML for phylogeny reconstruction
(Default: FastTree)
-zZ : Make zZ-formatted files
This additionally creates fasta/nwk files with zZ'uid'zZ format for names of each genome
-gsi_threshold: The threshold used for GSI calculations (1~100)
Even if the exact bipartition doesn't exist in a gene tree, it is regarded as a supported bipartition based on their similiarity
It is when the number of genomes more than specified threshold(percentage) of all genomes(leaves) support the topology of bipartition
A value of 95 or higher is recommended
(Default: 95)

---- Replacing labels -----
Replacing labels in a tree using metadata

java -jar UBCG.jar replace <run_id..trm> <gene>
ex) java -jar UBCG.jar replace 'run_id'.trm UBCG -taxon -strain
Making a UBCG tree file that uses both taxon_name and strain_name as labels
ex) java -jar UBCG.jar replace 'run_id'.trm rpoB -acc -taxon -type
Making a rpoB tree file that uses accession, taxon_name and strain_name as labels

Parameters
<run_id.trm> : A file containing trees with metadata. This file is automatically generated in the step 2
<gene> : The gene trees or UBCG tree you want to replace
-uid : add uids
-acc : add accessions
-label : add labels
-taxon : add taxon_names
-strain : add strain_names
-type : add type_info
-taxonomy : add taxonomy

---- Showing the content of bcg files ----
The content of bcg files (for example, gene sequences) can be viewed (as csv format that is readable by Microsoft Excel) by using the following command:

java -jar UBCG.jar view -i <a bcg file>
java -jar UBCG.jar view -d <directory containing bcg files>

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is download from https://www.ezbiocloud.net/tools/ubcg

=== System ===
64-bit Linux

Software

2022-11-02T19:57:21Z

Karen: /* Partial List of Installed Software */

,On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the [[Software on Sapelo2]] page.

Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in [[Software on Sapelo2]].

To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
<pre class="gcommand">
module spider
</pre>
You can also use the command above to search for a specific application. For more information, please see [[Lmod]].

'''Note:''' Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 600 software packages installed there. For more information, please see [[Software on Sapelo2]].

==Partial List of Installed Software==
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
'''Note:''' Click on the icons to the right of the column headings to sort the table.
[[#0|0-9]] [[#A|A]] [[#B|B]] [[#C|C]] [[#D|D]] [[#E|E]] [[#F|F]] [[#G|G]] [[#H|H]] [[#I|I]] [[#J|J]] [[#K|K]] [[#L|L]] [[#M|M]] [[#N|N]] [[#O|O]] [[#P|P]] [[#Q|Q]] [[#R|R]] [[#S|S]] [[#T|T]] [[#U|U]] [[#V|V]] [[#W|W]] [[#X|X]] [[#Y|Y]] [[#Z|Z]]
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" width="200px"| Name
! scope="col" class="unsortable" width="240px"| Version
! scope="col" width="160px"| Category
! scope="col" width="60px"| Cluster
! scope="col" width="20px"| Top
|-













| [[AlphaFold-Sapelo2|AlphaFold]] || 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.2.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[AMBER-Sapelo2|AMBER]] || 18, 22 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->








| [[anvi'o-Sapelo2|anvi'o]] || 4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:sapelo2|sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
















| [[basespace-cli-Sapelo2|basespace-cli]] || 1.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|| [[Beast-Sapelo2|Beast]] || 1.10.4, 2.6.2, 2.6.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[BionanoSolve-Sapelo2|BionanoSolve]] || 3.6.1-11162020 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



|[[Biopython-Teaching|Biopython]] || 1.75 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




| [[BLAST+-Sapelo2|BLAST+]] || 2.2.31, 2.9.0, 2.10.1,2.11.0,2.12.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] ||[[File:Up20.png|20px|link=#top]]
|- -->
| [[BLAST+-Teaching|BLAST+]] || 2.9.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-

| [[BLAST-Teaching|BLAST]] || 2.2.26 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Bowtie2-Teaching|Bowtie2]] || 2.3.5.1, 2.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[BUSCO-Sapelo2|BUSCO]] || 4.0.5, 4.0.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Canu-Sapelo2|Canu]] || 2.1.1|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[CellRanger-ATAC-Sapelo2|CellRanger-ATAC]] || 1.2.0, 2.0.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
































| [[cryoSPARC-Sapelo2|cryoSPARC]] || 3.3.1 || [[:Category:Engineering|Engineering]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->
|[[CUDA-Sapelo2|CUDA]] || 9.2.88, 10.1.243, 11.0.2, 11.1.1, 11.2.1 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Cytoscape-Teaching|Cytoscape]] || 3.7.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[EIGENSOFT-Teaching|EIGENSOFT]] || 7.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-




















































| [[GAUSSIAN-Sapelo2|GAUSSIAN]] || 09, 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
|[[GAUSSIAN-Teaching|GAUSSIAN]] || 16 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[GaussView-Sapelo2|GaussView]] || 5, 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[GaussView-Teaching|GaussView]] || 6.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[GEM-Sapelo2|GEM]] || 1.0, 1.1, 1.2, 1.4.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[GeneMarkES-Sapelo2|GeneMarkES]] || 4.57 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


































| [[GROMACS-Sapelo2 |GROMACS]] || 4.5.6,2019.4,2020,2020.3,2021.2,2021.3,2021.4 ||[[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



















| [[HISAT2-Teaching|HISAT2]] || 2.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[HpcGridRunner-Sapelo2|HPCGridRunner]] || 1.0.2 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->










|-
| [[iCommands-Sapelo2|iCommands]] || 4.2.8 || [[:Category:Tools|Tools]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[InterProScan-Sapelo2|InterProScan]] || 5.44-90.0, 5.51-85.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




| [[IQ-Tree-Teaching|IQ-Tree]] || 1.6.12|| [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-








| [[Java-Teaching|Java]] || 1.8.0_144, 1.8.0_241, 11.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-






| [[Jupyter-Sapelo2|Jupyter]] || 5.0.0, 5.6.0, 6.0.3 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Jupyter-Teaching|Jupyter]] || 6.0.2 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
|- -->













| [[LAMMPS-Sapelo2|LAMMPS]] || 3Mar2020 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-



































| [[Magma-Sapelo2|Magma]] || 2.25 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


| [[Maker-Sapelo2|Maker]] || 3.01.03 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[MATLAB-Sapelo2|MATLAB]] || R2019b, R2020a, R2020b, R2021a, R2021b || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-









| [[Medusa-Sapelo2 |Medusa]] || 1.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-






































| [[MOTECC_qmdcp-Teaching|MOTECC_qmdcp]] || 90 || [[:Category:Chemistry|Chemistry]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Mothur-Sapelo2|Mothur]] || 1.39.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[MrBayes-Sapelo2|MrBayes]] || 3.2.6, 3.2.7a || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-


















































| [[Ont-Guppy-Sapelo2|Ont-Guppy]] || 4.4.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[ORCA-Sapelo2 |ORCA]] || 4.2.1, 5.0.1 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->




|[[ORP-Sapelo2|ORP]] || 2.2.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[OrthoFinder-Sapelo2|OrthoFinder]] || 2.3.8, 2.3.11, 2.5.2 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->

| [[OrthoMCL-Sapelo2|OrthoMCL]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[PAML-Teaching|PAML]] || 4.9i || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->























| [[Perl-Teaching|Perl]] || 5.30.0 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[Phenix-Sapelo2|Phenix]] || 1.19.2-4158 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Pong-Sapelo2|Pong]] || 1.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]

























































|-
| [[Python-Sapelo2 |Python]] || 2.7.14, 2.7.15, 2.7.16, 3.7.4, 3.8.2, 3.8.6, 3.9.5 || [[:Category:Programming|Programming]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Python-Teaching|Python]] || 3.7.4, 2.7.16 || [[:Category:Programming|Programming]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->






| [[QIIME2-Sapelo2|QIIME2]] || 2019.10, 2020.2, 2020.6, 2020.11 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->







| [[R-Sapelo2 |R]] || 3.5.0, 3.6.2, 4.0.0, 4.1.0, 4.1.3, 4.2.1 ||[[:Category:Statistics|Statistics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-
| [[R-Teaching|R]] || 4.0.0 || [[:Category:Statistics|Statistics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[racon-Sapelo2 |Racon]] || 1.4.13 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-





| [[RAxML-Sapelo2 |RAxML]] || 8.2.11, 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[RAxML-Teaching|RAxML]] || 8.2.12 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->

















| [[RevBayes-Teaching|RevBayes]] || 1.1.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-







| [[Rosetta-Sapelo2 |Rosetta]] || 2020.28.61328, 2021.16.61629 || [[:Category:Chemistry|Chemistry]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->


| [[Rstudio-Sapelo2|Rstudio]] || 1.1.463, 1.2.5033, 1.4.1103, 2022.02.1-461, 2022.07.1-554 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-










| [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.9, 1.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|- -->































| [[smoke-Sapelo2|smoke]] || 4.7 || [[:Category:Other|Other]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-

































| [[SRAToolKit-Sapelo2 |SRAToolKit]] || 2.9.6-1,2.10.8,2.11.1 ||[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->













| [[StringTie-Teaching|StringTie]] || 2.1.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-
| [[Structure-Sapelo2|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->
| [[Structure-Teaching|Structure]] || 2.3.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]]
|-


































| [[Trinity-Sapelo2|Trinity]] || 2.5.1, 2.8.4, 2.8.5, 2.9.1, 2.10.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->



| [[UBCG-Sapelo2|UBCG]] || 3.0
|[[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|-














| [[Velvet-Sapelo2|Velvet]] || 1.2.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Sapelo2|Sapelo2]] || [[File:Up20.png|20px|link=#top]]
|- -->






















|}
[[#top|Back To Top]] [[File:Up20.png|20px|link=#top]]

[[Category:Sapelo2]][[Category:Teaching]][[Category:Software]]

BLAST Databases-Sapelo2

2022-10-20T20:28:03Z

Karen: fixed typo in db path

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]]

'''Blast databases'''

Blast databases are pre-formatted to work with blast commands from BLAST and BLAST+. These databases are similar to what you could build using the makeblastdb command with FASTA files. Each database is located at a directory with the name pattern /db/ncbiblast/year-month-date. For example, databases downloaded on February 01, 2022 will be available in /db/ncbiblast/20220201. The following databases are currently available and stored together with databases downloaded at the same time; nr, nt, taxdb, refseq_rna, refseq_protein, mouse_genome, human_genome and swissprot. The database refseq_genomic is no longer available to download as a pre-formatted database.

NCBI BLAST Datasets can be loaded just like software modules. This allows users to replicate results by always being able to use a time stamped version of a database. The time stamp corresponds to the download date of the dataset. To search for available NCBI BLAST dataset modules run the command:

<code>ml spider ncbiblastdb</code>

You can then load a database by running the command module load. For example to load the databases timestamped at 06/16/2021:

<code>module load ncbiblastdb/20210616</code>

Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20210616. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:
<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_BLAST+ 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out 
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err 

cd $SLURM_SUBMIT_DIR 
module load BLAST+/2.9.0-gompi-2019b 
module load ncbiblastdb/20220201 
blastn -query example.fasta -out results.out -db nt 
</div>

In your actual submission script, use your own discretion for the Slurm header values.

NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets '''every 3 months''' as well as other NCBI BLAST datasets: cdd_delta, human_genome, mouse_genome, nrte, refseq_protein, refseq_rna, swissprot, and taxdb datasets.

'''Blast database - old version 5'''

According to https://ncbiinsights.ncbi.nlm.nih.gov/tag/blastdbv5/, around Feb. 04, 2020 NCBI dropped the _v5 suffix for the v5 Blast databases.

An old version of the v5 database (download in June 2019) is located at a directory with name pattern as /db/ncbiblast.v5/''dbname'', where ''dbname'' is the name of the database, such as nr, nt, taxdb, refseq_rna, swissprot, etc.

These old versions of the nr and nt databases still have the _v5 suffix, i.e. they are called nr_v5 and nt_v5, respectively.

[[#top|Back to Top]]