Bowtie

Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-generation sequencers. This is the original Bowtie (Bowtie 1); for gapped alignment of longer reads see Bowtie2.

Bowtie

License

Free to use and open source under the Artistic License 2.0.

Available

Roihu: 1.3.1, via the bio-apps module.

Usage

Bowtie is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Bowtie module:

module load bio-apps/v202603
module load bowtie/1.3.1

First index the reference genome with bowtie-build (do this in a scratch directory):

bowtie-build genome.fa genome

Then align reads against the index:

bowtie -x genome reads.fq -S output.sam

Example batch script

#!/bin/bash
#SBATCH --job-name=bowtie
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load bowtie/1.3.1

bowtie-build genome.fa genome
bowtie -p $SLURM_CPUS_PER_TASK -x genome reads.fq -S output.sam

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk