Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

There are two versions of Bowtie available: Bowtie2 and Bowtie.  The more recent Bowtie2 program differs significantly from its ancestor Bowtie. For example the command line options are different for these two tools.


Version on CSC's Servers

Taito: 1.2.2, 1.1.1,
Chipster graphical user interface


On Taito

module load biokit


module load biokit/4.9.3

The biokit modules set up a set of commonly used bioinformatics tools, including Bowtie, Bowtie2, TopHat and Cufflinks. (Note however that there are bioinformatics tools in Taito, that have a separate setup commands.)

In typical bowtie run you first need to index the reference genome with bowtie-build command ( Note you should do this in $WRKDIR in stead of your home directory). For example;

bowtie-build genome.fa genome

Alternatively you can use chipster_genomes command to download pe-calclutaed bowtie2 indexes from the CSC Chiptser server to Taito:

chipster_genomes bowtie

When the reference genome has been dowloaded or indexed the actual alignment job can be launched with bowtie command. For example for single end reads this could be done with command:

bowtie genome reads.fq > output.sam

Usage in Taito

In Taito, bowtie and bowtie2 jobs should be run as batch jobs. Below is a sample batch job file, for running a bowtie job in Taito:

#!/bin/bash -l
#SBATCH -J bowtie
#SBATCH -o output_%j.txt
#SBATCH -e errors_%j.txt
#SBATCH -t 04:00:00
#SBATCH -n 1
#SBATCH --nodes=1  
#SBATCH --cpus-per-task=8
#SBATCH --mem=8000

module load biokit
bowtie-build genome.fasta genome
bowtie -p $SLURM_CPUS_PER_TASK genome reads.fq > output.sam

In the batch job example above one task (-n 1) is executed. The Bowtie2 job uses 8 cores (--cpus-per-task=8 ) with total of 8 GB of memory (--mem=8000). The maximum duration of the job is four hours (-t 04:00:00 ). All the cores are assigned from one computing node (--nodes=1 ).

You can submit the batch job file to the batch job system with command:

sbatch batch_job_file.bash

Check the chapter 3 of the Taito user guide for more information about running batch jobs.




When you use Bowtie, please cite:

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.



More information about Bowtie can be found from the Bowtie home page.