GenomeTools¶
GenomeTools are a collection of tools to analyse genome sequences.
GenomeTools are available as a module on Apocrita.
Usage¶
To run the default 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¶
Serial jobs¶
Here is an example job running on 1 core and 1GB of memory to calculate statistics for the given fasta file(s):
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load genometools
gt seqstat raw_data.fq.gz
Here is an example job running on 1 core and 1GB of memory to 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