Bowtie

From ScientificComputing
Jump to: navigation, search

Category

Bioinformatics, Aligner

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).

Available versions (Euler, old software stack)

Legacy versions Supported versions New versions
1.1.1

Environment modules (Euler, old software stack)

Version Module load command Additional modules loaded automatically
1.1.1 module load gcc/4.8.2 bowtie/1.1.1

How to submit a job

You can submit a bowtie job in batch mode with the following command:
bsub [LSF options] "bowtie [bowtie options]"
Here you need to replace [bowtie options] with bowtie command line options (please run bowtie -h for getting a list of all command line options) and [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system.

License information

Artistic license 1.0

Links

http://bowtie-bio.sourceforge.net/index.shtml

https://en.wikipedia.org/wiki/Bowtie_(sequence_analysis)
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-3-r25