Difference between revisions of "Breakway"
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* Empirically identifies structural variation breakpoints. | * Empirically identifies structural variation breakpoints. | ||
* Highly specific analysis generates very few false positives. | * Highly specific analysis generates very few false positives. | ||
| − | * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives. | + | * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives. |
| − | |bio domain=Whole Genome Resequencing, Genomics, Structural variants, InDel discovery, | + | |bio domain=Whole Genome Resequencing, Genomics, Structural variants, InDel discovery, |
|bio method=DNA sequence analysis, genetic variation annotation | |bio method=DNA sequence analysis, genetic variation annotation | ||
| − | |bio tech=SOLiD, Solexa, Cross-platform: supports color space and varied read lengths (from Helicos to 454), 454, Sanger | + | |bio tech=ABI SOLiD, Solexa, Cross-platform: supports color space and varied read lengths (from Helicos to 454), 454, Sanger |
|created by=Clark, MJ | |created by=Clark, MJ | ||
|created at=UCLA, Stanley F. Nelson Lab, Department of Human Genetics | |created at=UCLA, Stanley F. Nelson Lab, Department of Human Genetics | ||
Revision as of 20:44, 28 April 2010
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Application data |
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| Created by | Clark, MJ |
|---|---|
| Biological application domain(s) | Whole Genome Resequencing, Genomics, Structural variants, InDel discovery |
| Principal bioinformatics method(s) | DNA sequence analysis, genetic variation annotation |
| Technology | ABI SOLiD, Solexa, Cross-platform: supports color space and varied read lengths (from Helicos to 454), 454, Sanger |
| Created at | UCLA, Stanley F. Nelson Lab, Department of Human Genetics
Sourceforge |
| Maintained? | Yes |
| Input format(s) | BAM |
| Output format(s) | TXT |
| Software features | Fast, specific, UNIX pipes |
| Programming language(s) | Perl |
| Licence | GPL |
| Operating system(s) | UNIX/Linux, MacOS X, Windows (probably) |
Summary: Breakway is a suite of programs that take aligned genomic data and report structural variation breakpoints. Features include:
- Takes in BAM formatted input, the current standard for genomic alignments.
- Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera.
- Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera.
- Empirically identifies structural variation breakpoints.
- Highly specific analysis generates very few false positives.
- Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives.
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