bowtie2
Overview
Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes.
Version 2.1.0 binaries are available on the iCSF.
Bowtie 2 is not a “drop-in” replacement for Bowtie 1. Bowtie 2’s command-line arguments and genome index format are both different from Bowtie 1’s. See the section in the bowtie2 manual on how they differ.
Restrictions on use
All users may access and use Bowtie. The software is open source using the GPL3 license. Users should consult the following file for further information: $BOWTIE2_HOME/$BOWTIE2_VER/LICENSE
For citation information see the Bowtie2 website.
Set up procedure
To use the software you will need to load the modulefile:
module load apps/binapps/bowtie2/2.1.0
Indexes – No pre-built indexes have been installed. Users should download and build their own indexes and set the variable BOWTIE2_INDEXES on the command line or in .bashrc . For example, in your scratch area:
export BOWTIE2_INDEXES=$HOME/scratch/my_indexes
Running the application
Example
Create an index for the Lambda phage reference genome included with Bowtie 2, create a jobscript containing:
bowtie2-build $BT2_HOME/example/reference/lambda_virus.fa lambda_virus
Now use Bowtie 2 aligner (bowtie2), which aligns a set of unpaired reads to the Lambda phage reference genome using the index generated in the previous step.
bowtie2 -x lambda_virus -U $BT2_HOME/example/reads/reads_1.fq -S eg1.sam