Difference between revisions of "Bowtie"
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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. | + | * 0.12.x - BOWTIE_INDEXES - location of pre-built index files |
| − | * 2.0. | + | * 2.0.x - BOWTIE2_INDEXES - location of pre-built index files |
* Pre-built Bowtie indexes can be found in the <code>/project/bio/bowtie</code> directory. | * Pre-built Bowtie indexes can be found in the <code>/project/bio/bowtie</code> directory. | ||
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Revision as of 17:49, 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.
Required Modules
Serial
- bowtie
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
- 0.12.x - BOWTIE_INDEXES - location of pre-built index files
- 2.0.x - BOWTIE2_INDEXES - location of pre-built index files
- Pre-built Bowtie indexes can be found in the
/project/bio/bowtiedirectory.