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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.


To run the default installed version of Bowtie, simply load the bowtie module:

$ module load bowtie
$ bowtie -h

Usage:   bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> |
         --interleaved <i> | <s>} [<hit>]

For full usage documentation, run bowtie -h.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory:

#$ -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
# -c is the query sequence which will be used
bowtie -a -v 2 <inputDir> --suppress 1,5,6,7 -c ATGCATCATGCGCCAT