# bowtie2

## Summary

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