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.
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 or interactive session:
module load bowtie2