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Bowtie2 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. Bowtie2 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.


Free to use and open source under GNU GPLv3.


  • Puhti: 2.4.1, 2.4.4,
  • Chipster graphical user interface


In Puhti, Bowtie2 can be taken in use as part of the biokit module collection:

module load biokit
The biokit modules sets up a set of commonly used bioinformatics tools, including Bowtie2. (Note however that there are bioinformatics tools in Puhti, that have a separate setup commands.)

In typical bowtie2 run you first need to index the reference genome with bowtie2-build command. You should do this in scratch directory in stead of your home directory. For example;

bowtie2-build genome.fa genome
Alternatively you can use chipster_genomes command to download pe-calclutaed bowtie2 indexes from the CSC Chiptser server to Puhti:

chipster_genomes bowtie2
When the reference genome has been dowloaded or indexed the actual alignment job can be launched with bowtie2 command. For example for single end reads this could be done with command:

bowtie2 -x genome -U reads.fq -S output.sam

For paried end data the minimal bowtie2 syntax is:

bowtie2 -x genome -1 first_read_set.fq -2 second_read_set.fq -S output.sam

Example batch script for Puhti

In Puhti, bowtie and bowtie2 jobs should be run as batch jobs. Below is a sample batch job file, for running a Bowtie2 paired end alignment in Puhti. The recent Bowtie2 versions scale well, so you can effecteively use up to 16 cores in your batch job.

Note that the batch job file must definbe define the project that will be used. You cab check your current project with comamnd:

id -g

You can check all the projects that you belong to, with command:


Use MyCSC ( to obtain more specific information about a specific project.

#!/bin/bash -l
#SBATCH --job-name=bowtie2
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --time=04:00:00
#SBATCH --partition=small
#SBATCH --ntasks=1
#SBATCH --nodes=1  
#SBATCH --cpus-per-task=16
#SBATCH --account=project_123456
#SBATCH --mem=16000

module load biokit
bowtie2-build genome.fasta genome
bowtie2 -p $SLURM_CPUS_PER_TASK -x genome -1 reads_1.fq -2 reads_2.fq > output.sam

In the batch job example above one task (--ntasks 1) is executed. The Bowtie2 job uses 16 cores (--cpus-per-task=16 ) with total of 16 GB of memory (--mem=16000). The maximum duration of the job is four hours (--time 04:00:00 ). All the cores are assigned from one computing node (--nodes=1 ). In the example the project that will be used is project_123456. This value shuold be replaced by the name of your computing project.

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

sbatch batch_job_file.bash
See the Puhti user guide for more information about running batch jobs.


When you use Bowtie2, please cite:

Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.



More information about Bowtie2 can be found from the Bowtie2 home page.

Last update: October 10, 2022