Bowtie (sequence analysis)

Bowtie is an open source software package for aligning short DNA sequencing reads against large reference genomes, developed by Ben Langmead and colleagues at the University of Maryland beginning in 2009 and later maintained at Johns Hopkins University. It builds an index of the reference genome using the Burrows-Wheeler transform, which keeps memory use low, roughly 2.2 gigabytes for the full human genome, while still allowing very fast lookups. To find where a given read belongs, Bowtie runs a quality-aware, greedy, randomized depth-first search through the index and reports the first alignment it finds that meets the requested criteria, rather than exhaustively searching for the single best scoring alignment. This tradeoff of exhaustiveness for speed made Bowtie widely used in short read sequencing pipelines, and the paper describing it had accumulated more than 11,000 citations by 2017.