Difference between revisions of "Bowtie"
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Bowtie is a part of the [[Tuxedo]] suite. | Bowtie is a part of the [[Tuxedo]] suite. | ||
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| + | HPC pre-built Bowtie Indexes are located in ''/scratch/hpc/bio/bowtie''. They should be available for bowtie use automatically. | ||
<!--Location--> | <!--Location--> | ||
{{App_Location|app={{#var:app}}|{{#var:ver}}}} | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
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* HPC_BOWTIE_EX - examples directory | * HPC_BOWTIE_EX - examples directory | ||
* HPC_BOWTIE_SCR - scripts 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 | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
Revision as of 21:24, 15 November 2011
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