BOWTIE2 is a tool for fast and sensitive sequencing read alignment.

BOWTIE2 is a fast, memory-efficient tool for aligning sequencing reads
to long reference sequences. It is especially good for aligning reads
whose lengths are from 50 to hundreds or thousands of characters.
It is particularly good on relatively long genomes, such as those
of mammals.

BOWTIE2 indexes the genome with an FM Index to keep its memory footprint
small: thus, for the human genome, its memory footprint is typically
around 3.2 GigaBytes. BOWTIE2 supports gapped, local, and paired-end
alignment modes.

Web Site:

The BOWTIE2 web page at SourceForge:



On any ARC cluster, check the installation details
by typing "module spider bowtie2".

BOWTIE2 requires that the appropriate modules be loaded before it can
be used. One version of the appropriate commands for use on NewRiver is:

module purge
module load gcc/5.2.0
module load bowtie2/2.2.5


The following batch file applies BOWTIE2 to data in a FASTQ file:

#! /bin/bash
#PBS -l walltime=0:05:00
#PBS -l nodes=1:ppn=1
#PBS -W group_list=newriver
#PBS -q open_q
#PBS -j oe
module purge
module load gcc/5.2.0
module load bowtie2/2.2.5
bowtie2 -x e_coli -U sim_reads.fq -S sim_reads_aligned.sam 

The full set of files for the BPWTIE2 example is too large to post on our system.
A partial set of files to carry out a similar process are available in