Difference between revisions of "Breakway"
(Created page with '{{Bioinformatics application |sw summary=Breakway is a suite of programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in …') |
Alperyilmaz (talk | contribs) |
||
| Line 17: | Line 17: | ||
|output format=TXT | |output format=TXT | ||
|sw feature=Fast, specific, UNIX pipes | |sw feature=Fast, specific, UNIX pipes | ||
| − | |language= | + | |language=Perl |
|licence=GPL | |licence=GPL | ||
|os=UNIX/Linux, MacOS X, Windows (probably) | |os=UNIX/Linux, MacOS X, Windows (probably) | ||
}} | }} | ||
Revision as of 18:50, 28 April 2010
|
Application data |
|
| 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 | 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.
"Error: no local variable "counter" was set." is not a number.
