Bowtie

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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

Legacy versions Supported versions New versions
1.1.1

Environment modules

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