Bowtie2

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.

• http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

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

Version 2.2.4 - Oct 22, 2014

• Fixed a Mavericks OSX specific bug caused by some linkage ambiguities.
• Added lz4 compression option for the wrapper.
• Fixed the vanishing --no-unal help line.
• Added the static linkage for MinGW builds.
• Added extra seed-hit output.
• Fixed missing 0-length read in fastq --passthrough output.
• Fixed an issue that would cause different output in -a mode depending on random seed.