Bowtie

Introduction

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).

For more information, please check its website: https://biocontainers.pro/tools/bowtie and its home page: http://bowtie-bio.sourceforge.net/.

Versions

  • 1.3.1

Commands

  • bowtie

  • bowtie-build

  • bowtie-inspect

Module

You can load the modules by:

module load biocontainers
module load bowtie

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 Bowtie on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bowtie
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers bowtie

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