SRMA - short read micro re-aligner | Tool name | SRMA - short read micro re-aligner |
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| URL | http://srma.sourceforge.net |
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| Important features | 1. SRMA is a short read micro re-aligner for next-generation high throughput sequencing data.
2. This tool aims to perform a re-alignment of each read to a graphical representation of all alignments within a local region to provide a better overall base-resolution consensus.
3. SRMA does not support enumerating over insertions or deletions caused by homopolymer errors that can be found in 454 data and other flow-based technologies. |
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| Citations | Homer N, Nelson SF.
Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA.
Genome Biol. 2010;11(10):R99. Epub 2010 Oct 8.
PMID: 20932289 |
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| Year of publication | 2010 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | Realignment, SNP discovery, Indel discovery |
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| Category | Free, Downloadable |
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| License | GPL |
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| Status | |
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| Input file format | SAM, BAM |
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| Output file format | SAM, BAM |
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| Operating system | |
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| Operating language | Java/C |
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| Platform | Illumina/Solexa, ABI SOLiD, Roche 454 |
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