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.
The following versions of Bowtie2 are available on OSC clusters:
Version | Owens | Pitzer | Note |
---|---|---|---|
2.2.9 | X | ||
2.3.4.3 | X | ||
2.4.1 | X* | X* | Python 3 rqeuired for all python scripts |
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.
Bowtie2 is available to all OSC users. If you have any questions, please contact OSC Help.
Ben Langmead et al., Open source
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.module load bowtie2
. The default version will be loaded.