Difference between revisions of "SHOREmap"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=Extension of the short read analysis pipeline SHORE. SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants. | |sw summary=Extension of the short read analysis pipeline SHORE. SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants. | ||
| − | |bio tech=Illumina, SOLiD, | + | |bio tech=Illumina, ABI SOLiD, |
|created at=MPI, | |created at=MPI, | ||
|maintained=Yes | |maintained=Yes | ||
|input format=shore consensus files | |input format=shore consensus files | ||
|output format=pdf, text | |output format=pdf, text | ||
| − | |language=Perl, R, | + | |language=Perl, R, |
| − | |licence=GPLv3, | + | |licence=GPLv3, |
}} | }} | ||
== Description == | == Description == | ||
Revision as of 02:49, 5 January 2012
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Application data |
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| Technology | Illumina, ABI SOLiD |
|---|---|
| Created at | MPI |
| Maintained? | Yes |
| Input format(s) | shore consensus files |
| Output format(s) | pdf, text |
| Programming language(s) | Perl, R |
| Licence | GPLv3 |
Summary: Extension of the short read analysis pipeline SHORE. SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants.
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Description
SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants. SHOREmap requires aligned sequence data from a pooled mapping population. Based on the read count at marker positioning distinguishing the parents it recognizes regions with skews in the allele distribution. Annotating the changes within this interval rapidly leads to identification of the causal changes.
Initially designed for candidate gene identification in the plant model species Arabidopsis, in principle, SHOREmap should be usable for other species as well.
Links
- SHOREmap Homepage [ edit link ]
- SHOREmap Manual [ edit link ]
- SHOREmap Publication full text [ edit link ]
References
To add a reference for SHOREmap, enter the PubMed ID in the field below and click 'Add'.
Search for "SHOREmap" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
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