Bowtie 2


``Bowtie 2``is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

For more information, please check its website: and its home page on Github.


  • 2.4.2

  • 2.5.1


  • bowtie2

  • bowtie2-build

  • bowtie2-inspect


You can load the modules by:

module load biocontainers
module load bowtie2

Example job


Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Bowtie 2 on our clusters:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -n 1
#SBATCH --job-name=bowtie2
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers bowtie2

bowtie2-build ref.fasta ref
bowtie2 -p 4 -x ref -1 input_1.fq -2 input_2.fq -S test.sam