Bowtie 2

Bowtie 2 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.

 

Documentation

 

Usage

 

To see what versions of Bowtie 2 are available type

module avail bowtie2

 

To see what other modules are needed, what commands are available and how to get additional help type

module help bowtie2

 

To run Bowtie 2, include a command like this in your job script:

module load bowtie2

 

User Information

Passwords
Connect to PSC systems:
Policies
Technical questions:

Send mail to remarks@psc.edu or call the PSC hotline: 412-268-6350.