Genometools

Notitle

Genometools are a collection of tools to analyse genome sequences.

Genometools are available as a module on Apocrita.

Usage

To run the latest installed version of Genometools, simply load the genometools module:

module load genometools
$ gt -help
Usage: gt [option ...] [tool | script] [argument ...]
The GenomeTools genome analysis system.

-i       enter interactive mode after executing 'tool' or 'script'
-q       suppress warnings
-test    perform unit tests and exit
-seed    set seed for random number generator manually.
         0 generates a seed from current time and process id
-version display version information and exit

To display the list of available tools, execute gt -help.

Example jobs

Here are a couple of example jobs both running on 1 core and 1GB of memory:

Sequence Status

Calculate statistics for fasta file(s).

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=0:10:0
#$ -l h_vmem=1G

module load genometools
gt seqstat raw_data.fq.gz

Sequence Extraction

Extract sequences from given sequence file(s) or fastaindex into the following files: .des, .esq, .md5, .ois, .sds and .ssp.

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load genometools
gt extractseq raw_data.fq.gz

References

List of websites for project page, manuals, tutorials etc.