Difference between revisions of "SRMA"
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{{Bioinformatics application | {{Bioinformatics application | ||
| − | |sw summary= | + | |sw summary=SRMA is a short read micro re-aligner for next-generation high throughput sequencing data. |
| − | |bio domain=SNP | + | |bio domain=SNP detection, Indel detection |
| − | |bio method= | + | |bio method=Localised reassembly |
| + | |bio tech=Illumina, ABI SOLiD, 454 | ||
| + | |created by=Nils Homer | ||
| + | |created at=University of California, Los Angeles | ||
|maintained=Yes | |maintained=Yes | ||
| − | |input format=SAM | + | |email address=nhomer@cs.ucla.edu |
| + | |input format=SAM, BAM | ||
| + | |output format=SAM, BAM | ||
| + | |language=Java, C | ||
| + | |licence=GPL | ||
}} | }} | ||
== Description == | == Description == | ||
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| + | SRMA is a short read micro re-aligner for next-generation high throughput sequencing data. | ||
| + | Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed indels. 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. | ||
| − | + | Currently this tool works well with and has been tested on 30x diploid coverage genome sequencing data from Illumina and ABI SOLiD technology. This tool may not work well with 454 data, as indels are a significant error mode for 454 data. | |
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{{Links}} | {{Links}} | ||
{{References}} | {{References}} | ||
{{Link box}} | {{Link box}} | ||
Latest revision as of 19:59, 19 December 2015
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Application data |
|
| Created by | Nils Homer |
|---|---|
| Biological application domain(s) | SNP detection, Indel detection |
| Principal bioinformatics method(s) | Localised reassembly |
| Technology | Illumina, ABI SOLiD, 454 |
| Created at | University of California, Los Angeles |
| Maintained? | Yes |
| Input format(s) | SAM, BAM |
| Output format(s) | SAM, BAM |
| Programming language(s) | Java, C |
| Licence | GPL |
| Contact: | nhomer@cs.ucla.edu |
Summary: SRMA is a short read micro re-aligner for next-generation high throughput sequencing data.
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Description
SRMA is a short read micro re-aligner for next-generation high throughput sequencing data.
Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed indels. 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.
Currently this tool works well with and has been tested on 30x diploid coverage genome sequencing data from Illumina and ABI SOLiD technology. This tool may not work well with 454 data, as indels are a significant error mode for 454 data.
Links
References
To add a reference for SRMA, enter the PubMed ID in the field below and click 'Add'.
Search for "SRMA" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
