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Bowtie 2

Memory-efficient tool for aligning sequencing reads to long reference sequences

Homepage Version(s): 2.5.4

Bowtie 2 requires an environment module

In order to use Bowtie 2, you must first load the appropriate environment module: 

module load gnu

Bowtie 2 is a bioinformatics program designed to align genomic sequence reads of about 50 and up to thousands of characters in length. It is particularly good for aligning such reads to fairly long genomes, such as mammalian genomes.

Using Bowtie 2 on RCC Resources#

Running Bowtie 2 on the HPC#

The following example shows the use of basic Bowtie2 commands. Download the example data files: e_coli_1000.fa and e_coli_1000.fq. Then run the commands:

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$ module load gnu
$ bowtie2-build e_coli_1000.fa e_coli

This should print many lines of output and then quit. When the command completes, the current directory will contain six new files that all start with e_coli and end with .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, and .rev.2.bt2. These files constitute the index. To run the Bowtie 2 aligner, which aligns a set of unpaired reads to the E. coli reference genome using the index generated in the previous step, use the command:

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$ bowtie2 -x e_coli -U e_coli_1000.fq -S eg1.sam

The alignment results in SAM format are written to the file eg1.sam, and a short alignment summary is written to the console.

Running Bowtie 2 in Parallel on HPC#

Below is a script to run the above example on the HPC using the Slurm job scheduler. The script must be saved with the .sh extension.

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#!/bin/bash
#SBATCH -p genacc_q
#SBATCH -J Bowtie2Job
module load gnu
bowtie2-build e_coli_1000.fa e_coli
bowtie2 -x e_coli -U e_coli_1000.fq -S eg1.sam

Then submit your script using the following command, replacing YOURSCRIPT with the name of your script file:

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$ sbatch YOURSCRIPT.sh