Bowtie (sequence analysis)
Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics.[1]
History
The Bowtie sequence aligner was originally developed by Ben Langmead et al. at the University of Maryland in 2009.[1] The aligner is typically used with short reads and a large reference genome, or for whole genome analysis. Bowtie is promoted as "an ultrafast, memory-efficient short aligner for short DNA sequences." The speed increase of Bowtie is partly due to implementing the Burrows–Wheeler transform for aligning, which reduces the memory footprint (typically to around 2.2GB for the human genome);[2] a similar method is used by the BWA[3] and SOAP2[4] alignment methods. The latest version of Bowtie (1.1.2) was released on June 23, 2015.[2] As of 2015, the Genome Biology paper describing the original Bowtie method has been cited more than 6,000 times.[1] Bowtie is open-source software and is currently maintained by Johns Hopkins University.
Bowtie is used as a sequence aligner by a number of other related bioinformatics algorithms, including TopHat,[5] Cufflinks[6] and the CummeRbund Bioconductor package.[7]
Bowtie 2
On 16 October 2011, the developers released a beta fork of the project called Bowtie 2.[8] 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. The latest version (2.2.6) was released on July 22, 2015.[9]
References
- 1 2 3 Langmead, Ben; Cole Trapnell; Mihai Pop; Steven L Salzberg (4 March 2009). "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome" (PDF). Genome Biology. 10 (3): 10:R25. doi:10.1186/gb-2009-10-3-r25. PMC 2690996
. PMID 19261174. Retrieved 29 November 2013. - 1 2 "Bowtie: An ultrafast, memory-efficient short read aligner - SourceForge". Retrieved 29 November 2013.
- ↑ Li, H.; Durbin, R. (18 May 2009). "Fast and accurate short read alignment with Burrows-Wheeler transform". Bioinformatics. 25 (14): 1754–1760. doi:10.1093/bioinformatics/btp324. PMC 2705234. PMID 19451168.
- ↑ Li, R.; Yu, C.; Li, Y.; Lam, T.-W.; Yiu, S.-M.; Kristiansen, K.; Wang, J. (3 June 2009). "SOAP2: an improved ultrafast tool for short read alignment". Bioinformatics. 25 (15): 1966–1967. doi:10.1093/bioinformatics/btp336. PMID 19497933.
- ↑ Trapnell, C.; Pachter, L.; Salzberg, S. L. (16 March 2009). "TopHat: discovering splice junctions with RNA-Seq". Bioinformatics. 25 (9): 1105–1111. doi:10.1093/bioinformatics/btp120. PMC 2672628. PMID 19289445.
- ↑ Trapnell, Cole; Roberts, Adam; Goff, Loyal; Pertea, Geo; Kim, Daehwan; Kelley, David R; Pimentel, Harold; Salzberg, Steven L; Rinn, John L; Pachter, Lior (1 March 2012). "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks". Nature Protocols. 7 (3): 562–578. doi:10.1038/nprot.2012.016. PMC 3334321. PMID 22383036.
- ↑ "CummeRbund - An R package for persistent storage, analysis, and visualization of RNA-Seq from cufflinks output". Retrieved 11 August 2015.
- ↑ Langmead, Ben; Salzberg, Steven L (4 March 2012). "Fast gapped-read alignment with Bowtie 2". Nature Methods. 9 (4): 357–359. doi:10.1038/nmeth.1923. PMID 22388286.
- ↑ "Bowtie 2: fast and sensitive read alignment". Retrieved 11 August 2015.