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 Oakley Owens pitzer
1.1.2 X* 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 without restriction.

Publisher/Vendor/Repository and License Type

Ben Langmead et al., Open source (Artistic 2.0)

Usage

Usage on Oakley

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 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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