bowtie2

Summary

Module Name: bowtie2
Support Level: Primary Support
Software Access Level: Open Access
Home Page: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Software Description

No description provided.

General Linux

To load this module for use in a Linux environment, you can run the command:

module load bowtie2

Depending on where you are working, there may be more than one version of bowtie2 available. To see which modules are available for loading you can run:

module avail bowtie2

Slurm Example

#!/bin/bash
#SBATCH --job-name="rfm_RunBowtie2Test_job"
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=rfm_RunBowtie2Test_job.out
#SBATCH --error=rfm_RunBowtie2Test_job.err
#SBATCH --time=0:10:0
#SBATCH -p msismall
module load bowtie2/2.3.4.1
wget https://public.s3.msi.umn.edu/reframe/sw/bwa/sample.fq
wget https://public.s3.msi.umn.edu/reframe/sw/bwa/ref.fasta
bowtie2-build ref.fasta ref
bowtie2 -x ref sample.fq -S sample.sam