GET HOMOLOGUES-Teaching
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Category
Bioinformatics
Program On
Teaching
Version
1.7.6
Author / Distributor
Description
"a versatile software package for pan-genome analysis.". More details are at GET_HOMOLOGUES
Running Program
- Version 1.7.6, installed at /usr/local/apps/gb/GETHOMOLOGUES/1.7.6
To use this version, please load the module with
ml GETHOMOLOGUES/1.7.6
ere is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_GLIMMER
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=GLIMMER.%j.out
#SBATCH --error=GLIMMER.%j.err
cd $SLURM_SUBMIT_DIR
ml GETHOMOLOGUES/1.7.6
perl /usr/local/apps/gb/GETHOMOLOGUES/1.7.6/get_homologues.pl [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml GETHOMOLOGUES/1.7.6
perl /usr/local/apps/gb/GETHOMOLOGUES/1.7.6/get_homologues.pl -h
usage: /usr/local/apps/gb/GETHOMOLOGUES/1.7.6/get_homologues.pl [options]
-h this message
-v print version, credits and checks installation
-d directory with input FASTA files ( .faa / .fna ), (overrides -i,
GenBank files ( .gbk ), 1 per genome, or a subdirectory use of pre-clustered sequences
( subdir.clusters / subdir_ ) with pre-clustered sequences ignores -c, -g)
( .faa / .fna ); allows for new files to be added later;
creates output folder named 'directory_homologues'
-i input amino acid FASTA file with [taxon names] in headers, (required unless -d is set)
creates output folder named 'file_homologues'
Optional parameters:
-o only run BLAST/Pfam searches and exit (useful to pre-compute searches)
-c report genome composition analysis (follows order in -I file if enforced,
ignores -r,-t,-e)
-R set random seed for genome composition analysis (optional, requires -c, example -R 1234,
required for mixing -c with -c -a runs)
-s save memory by using BerkeleyDB; default parsing stores
sequence hits in RAM
-m runmode [local|cluster] (default local)
-n nb of threads for BLAST/HMMER/MCL in 'local' runmode (default=2)
-I file with .faa/.gbk files in -d to be included (takes all by default, requires -d)
Algorithms instead of default bidirectional best-hits (BDBH):
-G use COGtriangle algorithm (COGS, PubMed=20439257) (requires 3+ genomes|taxa)
-M use orthoMCL algorithm (OMCL, PubMed=12952885)
Options that control sequence similarity searches:
-X use diamond instead of blastp (optional, set threads with -n)
-C min %coverage in BLAST pairwise alignments (range [1-100],default=75)
-E max E-value (default=1e-05,max=0.01)
-D require equal Pfam domain composition (best with -m cluster or -n threads)
when defining similarity-based orthology
-S min %sequence identity in BLAST query/subj pairs (range [1-100],default=1 [BDBH|OMCL])
-N min BLAST neighborhood correlation PubMed=18475320 (range [0,1],default=0 [BDBH|OMCL])
-b compile core-genome with minimum BLAST searches (ignores -c [BDBH])
Options that control clustering:
-t report sequence clusters including at least t taxa (default t=numberOfTaxa,
t=0 reports all clusters [OMCL|COGS])
-a report clusters of sequence features in GenBank files (requires -d and .gbk files,
instead of default 'CDS' GenBank features example -a 'tRNA,rRNA',
NOTE: uses blastn instead of blastp,
ignores -g,-D)
-g report clusters of intergenic sequences flanked by ORFs (requires -d and .gbk files)
in addition to default 'CDS' clusters
-f filter by %length difference within clusters (range [1-100], by default sequence
length is not checked)
-r reference proteome .faa/.gbk file (by default takes file with
least sequences; with BDBH sets
first taxa to start adding genes)
-e exclude clusters with inparalogues (by default inparalogues are
included)
-x allow sequences in multiple COG clusters (by default sequences are allocated
to single clusters [COGS])
-F orthoMCL inflation value (range [1-5], default=1.5 [OMCL])
-A calculate average identity of clustered sequences, (optional, creates tab-separated matrix,
by default uses blastp results but can use blastn with -a recommended with -t 0 [OMCL|COGS])
-P calculate percentage of conserved proteins (POCP), (optional, creates tab-separated matrix,
by default uses blastp results but can use blastn with -a recommended with -t 0 [OMCL|COGS])
-z add soft-core to genome composition analysis (optional, requires -c [OMCL|COGS])
This program uses BLAST (and optionally HMMER/Pfam) to define clusters of 'orthologous'
genomic sequences and pan/core-genome gene sets. Several algorithms are available
and search parameters are customizable. It is designed to process (in a SGE computer
cluster) files contained in a directory (-d), so that new .faa/.gbk files can be added
while conserving previous BLAST results. In general the program will try to re-use
previous results when run with the same input directory.
Installation
Source code is obtained from GET_HOMOLOGUES
System
64-bit Linux