Bowtie2

Overview

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.

Using

Use the module name bowtie2 to discover versions available and to load the application.

Multicore:

The bowtie2 application can run across multiple threads. Look at the commands usage bowtie2 -h for further details on the --threads option.