GET HOMOLOGUES-Teaching
Jump to navigation
Jump to search
Category
Bioinformatics
Program On
Sapelo2
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
Here is an example of a shell script, sub.sh, to run on the batch queue:
#PBS -S /bin/bash #PBS -q batch #PBS -N j_gffread #PBS -l nodes=1:ppn=1:AMD #PBS -l walltime=4:00:00 #PBS -l mem=2gb cd $PBS_O_WORKDIR ml GETHOMOLOGUES/1.7.6<br> get_homologues.pl [options]
where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, and the job name need to be modified appropriately as well.
Submit the job to the queue with
qsub sub.sh
Documentation
ml 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