Difference between revisions of "Bowtie"
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* Bowtie does not align reads with indels. | * Bowtie does not align reads with indels. | ||
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| + | = Alternatives = | ||
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| + | [[BWA]] supports indels, but is a bit slower. | ||
{{Links}} | {{Links}} | ||
{{References}} | {{References}} | ||
{{Link box}} | {{Link box}} | ||
Revision as of 11:50, 14 September 2011
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Application data |
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| Created by | Ben Langmead, Cole Trapnell |
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| Principal bioinformatics method(s) | Mapping, Burrows-Wheeler, FM-Index |
| Created at | University of Maryland |
| Maintained? | Maybe |
| Input format(s) | FASTQ |
| Output format(s) | SAM |
| Operating system(s) | Mac OS X, Linux, Windows |
Summary: Bowtie is an ultrafast, memory-efficient short read aligner.
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Bowtie aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: 1.3 GB for the human genome. It supports alignment policies equivalent to Maq and SOAP but is much faster: about 35x faster than Maq and over 350x faster than SOAP when aligning to the human genome.
Limitations
- Bowtie does not align reads with indels.
Alternatives
BWA supports indels, but is a bit slower.
Links
References
To add a reference for Bowtie, enter the PubMed ID in the field below and click 'Add'.
Search for "Bowtie" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
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