Bowtie
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Application data |
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| Created by | Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg |
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| Principal bioinformatics method(s) | Read mapping, Genome indexing (Burrows-Wheeler) |
| Created at | University of Maryland, Johns Hopkins University |
| Maintained? | Yes |
| Input format(s) | FASTQ |
| Output format(s) | SAM |
| Software version | 1.1.2 |
| Operating system(s) | Mac OS X, Linux, Windows |
| Contact: | bowtie-bio-announce@lists.sourceforge.net |
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
- Bowtie1 only handles a limited number of indels. Bowtie 2 has no limit and can handle any number of indels as well as very long reads.
Alternatives
BWA and SOAP2 are the most popular alternatives. BWA is about 25% slower and slightly less sensitive. SOAP2 is comparable in speed but considerably less sensitive (aligning fewer reads).
Links
References
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| Web Search | Wiki Sites | Scientific |
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