Bowtie1

Bowtie1 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).

Availability and Restrictions

Versions

The following versions of Bowtie1 are available on OSC clusters:

Version Owens pitzer
1.1.2 X*  
1.2.2   X*
* Current default version

You can use module spider bowtie1 to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

Bowtie1 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 (Artistic 2.0)

Usage

Usage on Owens

Set-up

To configure your environment for use of Bowtie1, run the following command:  module load bowtie1. The default version will be loaded. To select a particular Bowtie1 version, use  module load bowtie/version. For example, use  module load bowtie1/1.1.2 to load Bowtie1 1.1.2.

Usage on Pitzer

Set-up

To configure your environment for use of Bowtie1, run the following command:  module load bowtie1. The default version will be loaded. 

Further Reading

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