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. The pre-built genomic indexes have been downloaded and made available to the users under this module. For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie. For relatively short reads (e.g. less than 50 bp) Bowtie is sometimes faster and/or more sensitive.

Version: 2.4.4 (G100) 2.2.9 (Marconi)

Availability: GALILEO100, MARCONI

Target: all

Official web site:

Related Commands:

To use Bowtie2 genome indexes:

module load

You can find the indexes in the dir $BW2INDEX

Help and Documentation:

You can find documentation on the system, with the command

module help bowtie2 

The manual is on the web at the original home page ( CINECA consultants can be reached through the address: