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
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
The BOWTIE2 web page at SourceForge:
The BOWTIE2 online manual:
The BOWTIE2 citation:
Ben Langmead, Steven Salzberg,
Fast gapped-read alignment with Bowtie 2,
Volume 9, pages 357-359, 2012.
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 # cd $PBS_O_WORKDIR # 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