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Bowtie2 is an ultra fast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Bowtie2 is available as a module on Apocrita.


To run the default version of Bowtie2, simply load the bowtie2 module:

$ module load bowtie2
$ bowtie2 -h

Usage:   bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> |
         --interleaved <i>} -S [<sam>]

For full usage documentation, run bowtie2 -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 bowtie2

# Prepare example genomes in <inputDir>
# Output is stored in <outputDir>
bowtie2-build <inputDir> <outputDir>
bowtie2-inspect <outputDir>