Bowtie

Description

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Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

Bowtie is a part of the Tuxedo suite.

HPC pre-built Bowtie Indexes are located in /scratch/hpc/bio/bowtie. They should be available for bowtie use automatically. Template:App Location

Available Versions

• 0.12.7 - Default.
• 2.2.0-beta3 - will become default when released as a final version.

Running the application using modules

To use bowtie with the environment modules system at HPC the following commands are available:

Get module information for bowtie:

$module spider bowtie

Load the default application module:

$module load bowtie

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_BOWTIE_DIR - directory where bowtie is located.
• HPC_BOWTIE_BIN - executable directory
• HPC_BOWTIE_DOC - documents directory
• HPC_BOWTIE_EX - examples directory
• HPC_BOWTIE_SCR - scripts directory
• 0.12.7 - BOWTIE_INDEXES - location of pre-built index files
• 2.0.0b3 - BOWTIE2_INDEXES - location of pre-built index files