Bowtie is an ultrafast, memory-efficient short read aligner geared
toward quickly aligning large sets of short DNA sequences (reads) to
large genomes. It aligns 35-base-pair reads to the human genome at a
rate of 25 million reads per hour on a typical workstation. Bowtie
indexes the genome with a Burrows-Wheeler index to keep its memory
footprint small: for the human genome, the index is typically about
2.2GB (for unpaired alignment) or 2.9GB (for paired-end or colorspace
alignment). Multiple processors can be used simultaneously to achieve
greater alignment speed. Bowtie can also output alignments in the
standard SAM format, allowing Bowtie to interoperate with other tools
supporting SAM, including the SAMtools consensus, SNP, and indel
callers.

If you use Bowtie for your published research, please cite:
Langmead B, Trapnell C, Pop M, Salzberg SL.
Ultrafast and memory-efficient alignment of short DNA sequences to
the human genome. Genome Biol 10:R25.
