Bowtie¶
Bowtie is an ultra fast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.
Bowtie is available as a module on Apocrita.
Usage¶
To run the default installed version of Bowtie, simply load the
bowtie module:
$ module load bowtie
$ bowtie -h
usage: bowtie [-h] [--verbose] [--debug] [--large-index]
...
For full usage documentation, run bowtie -h.
Example job¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load bowtie
# Prepare example genomes in <inputDir>
# Output is stored in current working directory
# -a reports all valid alignments per read or pair
# -v only accepts alignments with at most v <int> mismatches
# -x sets the basename of the Bowtie index to be searched
# -c is the query sequence which will be used
bowtie -a -v 2 -x <inputDir> --suppress 1,5,6,7 -c ATGCATCATGCGCCAT