Bowtie 2 is a tool for aligning short DNA sequence reads to a reference genome. The Bowtie algorithm uses a compressed full-text substring index based on the Burrows-Wheeler transform (BWT) technique and permits the use of multiple CPUs. Bowtie 2 can align reads up to thousands of nucleotides of length, has a gapped local alignment, and paired-end alignment modes.
Mapping; Bioinformatics; Genomics; Sequencing
Langmead B, Salzberg SL "Fast gapped-read alignment with Bowtie 2." Nat Methods. 2012 Mar 4;9(4):357-9. https://doi.org/10.1038/nmeth.1923
PMID: 22388286
PMCID: PMC3322381
Langmead B, Wilks C, Antonescu V, Charles R "Scaling read aligners to hundreds of threads on general-purpose processors." Bioinformatics. 2019 Feb 1;35(3):421-432. https://doi.org/10.1093/bioinformatics/bty648
PMID: 30020410
PMCID: PMC6361242
Flicek P "The need for speed. [Comment on Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. [Genome Biol. 2009]]" Genome Biol. 2009;10(3):212. https://doi.org/10.1186/gb-2009-10-3-212
PMID: 19344490
PMCID: PMC2690991
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