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. If you have additional indexes that could be of use to UF Biological Community please contact us and we'll add them to the reference file space. 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