bowtie

Overview

Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.

Version 0.12.9 & 1.0.0 binaries are available on the iCSF.

Restrictions on use

All users may access and use Bowtie. The software is open source. Users should consult the following file for further information: $BOWTIE_HOME/$BOWTIE_VER/COPYING

For citation information see the Bowtie website.

Set up procedure

To use the software you will need to load the modulefile:

module load apps/binapps/bowtie/1.0.0

module load apps/binapps/bowtie/0.12.9

Indexes – No pre-built indexes have been installed. Users should download and build their own indexes and set the variable BOWTIE_INDEXES on the command line or in .bashrc . For example, in your scratch area:

export BOWTIE_INDEXES=$HOME/scratch/my_indexes

Running the application

Examples

• Build the AF293 reference into the build format contig1.build

  bowtie-build AF293_REF.fasta contig1.build

• Run bowtie to build a file of reads that don’t map to contig1 (AF293):

  bowtie -S -q contig1.build C023MABXX_3_5_1.fastq 351.sam --un unmapped351.fastq
  

Further info

• Bowtie Manual