BBMap
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Application data |
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| Created by | Brian Bushnell |
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| Biological application domain(s) | Resequencing, Sequence alignment, Quality control, RNA-Seq alignment, Alternative splicing, Whole genome resequencing, SNP detection, Phylogenetics, Metagenomics, Read binning |
| Principal bioinformatics method(s) | Read mapping, RNA-Seq analysis, Sequence alignment, Sequence trimming, Sequence contamination filtering |
| Technology | Sanger, Illumina, 454, Ion Torrent, PacBio |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTQ, SAM, Scarf, FASTA+QUAL, paired, interleaved, gzip |
| Output format(s) | FASTA, FASTQ, SAM, FASTA+QUAL, gzip |
| Software features | Multithreaded. Faster and more accurate than competing aligners. Splice-aware. |
| Programming language(s) | Java 7 |
| Licence | BSD |
| Operating system(s) | Windows,
, Mac OS X, all supporting JVM |
| Contact: | bbushnell@lbl.gov |
Summary: 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.
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Description
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).
Links
References
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