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 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.

License

Artistic license (see /software/bowtie-0.12.8/src/COPYING) for bowtie and GNU GPL version 3 for bowtie2.

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of bowtie2 and load default version of bowtie2 as

module avail bowtie2/ # list available modules
module load bowtie2   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail bowtie2

and choose explicit version you want to use.

Documentation

http://bowtie-bio.sourceforge.net/index.shtml http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Homepage

http://bowtie-bio.sourceforge.net/index.shtml http://bowtie-bio.sourceforge.net/bowtie2/index.shtml