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.
Availability and Restrictions
Versions
The following versions of Bowtie2 are available on OSC clusters:
| Version | Owens | Pitzer | Cardinal | Note |
|---|---|---|---|---|
| 2.2.9 | X | |||
| 2.3.4.3 | X | |||
| 2.4.1 | X* | X* | Python 3 rqeuired for all python scripts | |
| 2.5.1 | X |
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 on Owens
Set-up
module load bowtie2. The default version will be loaded. To select a particular Bowtie2 version, use module load bowtie2/version. For example, use module load bowtie2/2.2.9 to load Bowtie2 2.2.9.Usage on Pitzer
Set-up
module load bowtie2. The default version will be loaded.