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 | Cardinal |
|---|---|---|---|
| 1.1.2 | X* | ||
| 1.2.2 | X* | ||
| 1.3.1 | 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. Usage on Cardinal
Set-up
To configure your environment for use of Bowtie1, run the following command:
module load bowtie. The default version will be loaded.
Further Reading
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