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.

Software Category: bio

For detailed information, visit the Bowtie2 website.

Available Versions

The current installation of Bowtie2 incorporates the most popular packages. To find the available versions and learn how to load them, run:

module spider bowtie2

The output of the command shows the available Bowtie2 module versions.

For detailed information about a particular Bowtie2 module, including how to load the module, run the module spider command with the module’s full version label. For example:

module spider bowtie2/2.1.0

Module Version Module Load Command
bowtie2 2.1.0 module load gcc/7.1.0 bowtie2/2.1.0
bowtie2 2.2.9 module load gcc/7.1.0 bowtie2/2.2.9

Build Your Own Version

Users may build their own versions of Bowtie2 if they wish to use a different compiler/MPI combination. Instructions are available on the Bowtie2 website.

SLURM Script Example

To run Bowtie2 on Rivanna, a script similar to the following can be used. Bowtie2 has many options so only a basic example is shown.