Bowtie2

Introduction

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:
BioContainers: https://biocontainers.pro/tools/bowtie2
Home page: https://github.com/BenLangmead/bowtie2

Versions

  • 2.4.2

  • 2.5.1

Commands

  • bowtie2

  • bowtie2-build

  • bowtie2-inspect

Example job

Warning

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 bowtie2 on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=bowtie2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load bowtie2/XXXX ### you can run *module avail bowtie2* to check all available versions

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