Bowtie
Application data |
|
Created by | Ben Langmead, Cole Trapnell |
---|---|
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.
"Error: no local variable "counter" was set." is not a number.
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 |
---|---|---|