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Short description:
Please summarise the application in a few sentences. Avoid links here. Bowtie is an ultrafast, memory-efficient short read aligner.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Read mapping, Genome indexing (Burrows-Wheeler),
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
University of Maryland, Johns Hopkins University
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).
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