Bowtie

Legacy documentation This page describes a service provided by a retired ACENET system. Most ACENET services are currently provided by national systems, for which please visit https://docs.computecanada.ca.

Description

Bowtie is a fast 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.

Modulefile

bowtie

Documentation

Bowtie2 homepage

Examples

$BOWTIE/example

Scripts

$BOWTIE/scripts

Usage

Here is an example of a submission script for Bowtie 2. It assumes you've already built the reference sequence:

#$ -cwd
#$ -l h_rt=01:00:00
#$ -pe openmp 4

module load bowtie
bowtie2 -p $NSLOTS -x lambda_virus -U $BOWTIE/example/reads/reads_1.fq -S eg1.sam