Difference between revisions of "Bowtie"
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Revision as of 16:30, 10 August 2012
Description
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.
Available Versions
- 0.12.7
- 0.12.8 - Default.
- 2.2.0-beta3 - will become default when released as a final version.
- 2.2.0-beta5 - new features since beta3. See bowtie2 for details.
Execution Environment and 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
- Pre-built Bowtie indexes can be found in the
/project/bio/bowtiedirectory.