[3] The source code for the package is distributed freely and compiled binaries are available for Linux, macOS and Windows platforms.
The Bowtie sequence aligner was originally developed by Ben Langmead et al. at the University of Maryland in 2009.
Bowtie is used as a sequence aligner by a number of other related bioinformatics algorithms, including TopHat,[8] Cufflinks[9] and the CummeRbund Bioconductor package.
[11] In addition to the Burrows-Wheeler transform, Bowtie 2 also uses an FM-index (similar to a suffix array) to keep its memory footprint small.
There is no upper limit on read length in Bowtie 2 and it allows alignments to overlap ambiguous characters in the reference.