SSAKE 3.5 (May 28, 2010)
v3.5+ Uses mate pairs to help resolve repeats (preventing contig misassemblies) at run time and attempts to force-fill gaps with redundant sequences (improves contiguity and repeat resolution).
For additional information about this project, please visit the overview page .
Available downloads
Release Notes
| State | Final release |
|---|---|
| License | GPL |
| Release Manager | Rene Warren |
In v3.5, the read pairing logic is used in the extension process. More specifically, passed the upper bound insert size, only forward reads AND reverse reads having their assembled mate already assembled in the contig being built will be considered for extension. This has for effect to mitigate contig misassemblies due to repeats. It will also extend the end of adjacent contigs in a scaffold in an effort to fill gaps - the resulting contigs are placed in the .mergedcontigs file.
