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. | ||
| − | HPC pre-built Bowtie Indexes are located in ''/ | + | HPC pre-built Bowtie Indexes are located in ''/scratch/lfs/bio/reference/bowtie''. They should be available for bowtie use automatically. If you have additional indexes that could be of use to others in the UF community please contact us and we'll add them to the reference file space. You can, of course build your own indexes for your own use, simply pass the path to those indexes in the bowtie command. |
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| + | We provide both [[Bowtie]] and [[Bowtie2]]. | ||
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<!--Modules--> | <!--Modules--> | ||
==Required Modules== | ==Required Modules== | ||
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===Serial=== | ===Serial=== | ||
*{{#var:app}} -loads the default Bowtie version | *{{#var:app}} -loads the default Bowtie version | ||
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==System Variables== | ==System Variables== | ||
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* HPC_BOWTIE_EX - examples directory | * HPC_BOWTIE_EX - examples directory | ||
* HPC_BOWTIE_SCR - scripts directory | * HPC_BOWTIE_SCR - scripts directory | ||
| − | * BOWTIE_INDEXES - | + | * BOWTIE_INDEXES - pre-built index files directory <code>/scratch/lfs/bio/reference/bowtie</code> |
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
Revision as of 13:26, 30 May 2014
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/lfs/bio/reference/bowtie. They should be available for bowtie use automatically. If you have additional indexes that could be of use to others in the UF community please contact us and we'll add them to the reference file space. You can, of course build your own indexes for your own use, simply pass the path to those indexes in the bowtie command.
We provide both Bowtie and Bowtie2.
Required Modules
Serial
- bowtie -loads the default Bowtie version
System Variables
- HPC_{{#uppercase:bowtie}}_DIR - installation directory
- HPC_BOWTIE_BIN - executable directory
- HPC_BOWTIE_DOC - documents directory
- HPC_BOWTIE_EX - examples directory
- HPC_BOWTIE_SCR - scripts directory
- BOWTIE_INDEXES - pre-built index files directory
/scratch/lfs/bio/reference/bowtie
Additional Information
Note: If your data is compressed your job script should add another ppn to accommodate the external gzip process that bowtie will run. To be safe, add another ppn in any case.
PBS Script Examples
See the Bowtie_PBS page for bowtie PBS script examples.