Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
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.
Bowtie version 0.12.8 and 0.12.9. Bowtie2 version 2.1.0, 2.2.3, 2.2.4, 2.2.9 and 2.3.0
module add bowtie-0.12.8 bowtie
module add bowtie2-2.3.0 bowtie2
for details see Documentation.
Artistic license (see /software/bowtie-0.12.8/src/COPYING) for bowtie and GNU GPL version 3 for bowtie2.