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Short description:
Please summarise the application in a few sentences. Avoid links here. BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Resequencing, Sequence alignment, Quality control, RNA-Seq alignment, Alternative splicing, Whole genome resequencing, SNP detection, Phylogenetics, Metagenomics, Read binning
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Read mapping, RNA-Seq analysis, Sequence alignment, Sequence trimming, Sequence contamination filtering,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Sanger, Illumina, 454, Ion Torrent, PacBio,
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):
== Description == <!-- Describe the application in the space below --> Uses a short kmers to rapidly index genome; no size or scaffold count limit. Much higher sensitivity and specificity than Burrows-Wheeler aligners, with similar or greater speed. Performs affine-transform-optimized global alignment, which is more accurate than Smith-Waterman. Handles Illumina, 454, PacBio, Sanger, and Ion Torrent data. Splice-aware; capable of processing long indels and RNA-seq, and producing Cufflinks-compatible sam tags. Pure Java; runs on any platform. Used by the Joint Genome Institute. BBMap is precompiled and is easy to launch via included shellscripts, but can also be run on systems that can't process bash scripts using the java command (instructions in the readme). <!-- -->
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