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 CSF.

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

Please do not run bowtie commands on the login node. qrsh is recommended for some commands. Computationally intense work should be done via the batch system.

Examples

• Build the AF293 reference into the build format contig1.build using the 1 hour compute node via qrsh:

  qrsh -V -l inter -l short -cwd bowtie-build AF293_REF.fasta contig1.build

• Run bowtie to builds a file of reads that don’t map to contig1 (AF293) using 8 cores via the batch system on the 1 hour node by writing a batch submission script:

       
  #$ -V
  #$ -cwd
  #$ -pe smp.pe 8
  #$ -l short
  
  bowtie -S -q -p $NSLOTS contig1.build C023MABXX_3_5_1.fastq 351.sam --un unmapped351.fastq
  

• and submitting it thus:

       
  qsub scriptname
  

• remove -l short if your job requires more than 1 hour. Perhaps replace with -l twoday.

Further info

• Bowtie Manual
• Related applications available on the CSF:
• Bowtie2
• Cufflinks
• Samtools
• Tophat