Difference between revisions of "Bowtie"

Revision as of 02:31, 18 May 2017

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.

Note

If you are using bowtie we installed you do not need to specify the path, only the database name. If you are using some other software and must specify the full path use '/ufrc/data/reference/bowtie'

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

modules documentation

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.

@@ Line 21: / Line 21: @@
 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.
+;Note:
+If you are using bowtie we installed you do not need to specify the path, only the database name. If you are using some other software and must specify the full path use '<code>/ufrc/data/reference/bowtie</code>'
+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]].