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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

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

More information