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.

NOTE!
This is an older version of the program, kept here for compatibility
with Ugene. You can safely install it along the new one. When you start
Ugene, go to Settings > Preferences > External Tools and manually select
the legacy binaries in /usr/bin/

Please cite:
Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2.
Nature Methods. 2012, 9:357-359.