bowtie2
Genetics
Software Description
Info
Module Name
bowtie2
Last Updated On
10/23/2023
Support Level
Primary Support
Software Access Level
Open Access
Home Page
Documentation
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 small,large,ram256g,ram1t
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
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
Agate Modules
Default
2.2.4_gcc-4.9.2_haswell
Other Modules
2.2.4_gcc-4.9.2_haswell, 2.3.4.1.CentOS7, 1.1.2, 2.1.0, 2.2.2, 2.2.4, 2.3.0, 2.3.1, 2.3.2, 2.3.4.1, 2.4.4
Mangi Modules
Default
2.3.4.1.CentOS7
Other Modules
2.3.4.1.CentOS7, 1.1.2, 2.1.0, 2.2.2, 2.2.4, 2.3.0, 2.3.1, 2.3.2, 2.3.4.1, 2.4.4
Mesabi Modules
Default
2.2.4_gcc-4.9.2_haswell
Other Modules
2.2.4_gcc-4.9.2_haswell, 2.3.4.1.CentOS7, 1.1.2, 2.1.0, 2.2.2, 2.2.4, 2.3.0, 2.3.1, 2.3.2, 2.3.4.1, 2.4.4