Bowtie
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 /project/bio/bowtie (or /project/bio/bowtie2' for Bowtie2)'. 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 have both Bowtie and Bowtie2 installed on the cluster. As Bowtie2 is still in beta stage, the default module is 0.12.8.
Required Modules
Serial
- bowtie -loads the default Bowtie version
- bowtie/2.0.0b6 - loads the Bowtie2 enviroment
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 - location of pre-built index files for 0.12.x versions:
/project/bio/bowtie - BOWTIE2_INDEXES - location of pre-built index files for 2.0.x versions:
/project/bio/bowtie2
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.