Difference between revisions of "Bowtie"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=Bowtie is an ultrafast, memory-efficient short read aligner. | |sw summary=Bowtie is an ultrafast, memory-efficient short read aligner. | ||
| − | |bio method= | + | |sw version=1.1.2 |
| − | |created by=Ben Langmead, Cole Trapnell | + | |bio method=Read mapping, Genome indexing (Burrows-Wheeler), |
| − | |created at=University of Maryland | + | |created by=Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg |
| + | |created at=University of Maryland, Johns Hopkins University | ||
| + | |maintained=Yes | ||
| + | |email address=bowtie-bio-announce@lists.sourceforge.net | ||
|input format=FASTQ, | |input format=FASTQ, | ||
|output format=SAM | |output format=SAM | ||
| Line 11: | Line 14: | ||
= Limitations = | = 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. | |
| − | * Bowtie | ||
= Alternatives = | = 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). | |
| − | [[BWA]] | ||
| − | |||
{{Links}} | {{Links}} | ||
{{References}} | {{References}} | ||
{{Link box}} | {{Link box}} | ||
Latest revision as of 22:09, 19 December 2015
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Application data |
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| Created by | Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg |
|---|---|
| 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
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 |
|---|---|---|
