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.