Bowtie2

Bowtie2 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. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Please note that bowtie (and tophat) CANNOT run in parallel, that is, on multiple nodes.  Submitting multi-node jobs will only waste resources.  In addition you must explicitly include the '-p' option to use multiple threads on a single node.

Availability and Restrictions

Versions

The following versions of Bowtie2 are available on OSC clusters:

Version Pitzer Ascend Cardinal Note
2.5.1 X X X*  
* Current default version

You can use module spider bowtie2 to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Bowtie2 is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

Ben Langmead et al., Open source

Usage

Usage

Set-up

To configure your environment for use of Bowtie2, run the following command: module load bowtie2/2.5.1.

Further Reading

Tag: 
bowtie2 bioinformatics biology
Supercomputer: 
Ascend
Cardinal
Pitzer
Service: 
Software
Fields of Science: 
Bioinformatics & Biology