Bowtie (sequence analysis)
Original author(s) | Ben Langmead Cole Trapnell Mihai Pop Steven Salzberg |
---|---|
Developer(s) | Ben Langmead et al., |
Stable release | |
Windows | |
Type | Bioinformatics |
Website | www |
Bowtie is a software package commonly used for
History
The Bowtie sequence aligner was originally developed by
Bowtie conducts a quality-aware, greedy, randomized, depth-first search through the space of possible alignments. Because the search is greedy, the first valid alignment encountered by Bowtie will not necessarily be the 'best' in terms of the number of mismatches or in terms of quality.
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.[10]
Bowtie 2
On 16 October 2011, the developers released a beta fork of the project called Bowtie 2.[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. Due to its implementation, Bowtie 2 is more suited to finding longer, gapped alignments in comparison with the original Bowtie method. There is no upper limit on read length in Bowtie 2 and it allows alignments to overlap ambiguous characters in the reference.
References
- ^ "Bowtie: An ultrafast, memory-efficient short read aligner". bowtie-bio.sourceforge.net. Retrieved 2021-03-28.
- ^ "Bowtie 2: fast and sensitive read alignment". bowtie-bio.sourceforge.net. Retrieved 2021-03-28.
- ^ PMID 19261174.
- S2CID 6200428.
- ^ a b "Bowtie: An ultrafast, memory-efficient short read aligner - SourceForge". Retrieved 29 November 2013.
- PMID 19451168.
- PMID 19497933.
- PMID 19289445.
- PMID 22383036.
- ^ "CummeRbund - An R package for persistent storage, analysis, and visualization of RNA-Seq from cufflinks output". Retrieved 11 August 2015.
- PMID 22388286.