Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences


Bowtie2 is a bioinformatics program designed to align genomic sequence reads of between 50 and up to thousands of charachters in length. It is particularly good for aligning such reads to fairly long genomes such as mammalian genomes.

Serially Running Bowtie2 on Spear

Following example shows the use of basic Bowtie2 commands.

First, we need some data. Download e_coli_1000.fa file. Then run the command,

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 four 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 Bowtie2 aligner, which aligns a set of unpaired reads to the e coli reference genome using the index generated in the previous step,

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.

Parallaly Running Bowtie2 on HPC

Following script shows how to run the above example on HPC using SLURM job scheduler.


#SBATCH -p genacc_q
#SBATCH -J Bowtie2Job

bowtie2-build e_coli_1000.fa e_coli
bowtie2 -x e_coli -U e_coli_1000.fq -S eg1.sam

Refer to Bowtie2 manual for more information about Bowtie2 commands.