SDquest

Version: 0.1

SDquest is a program for detection and analysis of segmental duplications (SDs) in large genomes. SDquest detects and decomposes mosaic SDs into elementary SDs, and further constructs the breakpoint graph of these mosaic SDs.

Download

Please download code in the "Code" folder, and download information of pairwise SDs (mosaic SDs) for human, gorilla and mouse genome in "Pairwise_SDs" ("Mosaic_SDs") folder. Refer to the Download.md file for details.

Usage

See the USAGE.md file.

Publications

Lianrong Pu, Yu Lin and Pavel Pevzner, "Detection and analysis of ancient segmental duplications in mammalian genomes", Submitted.

Third-party

SDquest package includes some third-party software:

• DSK [https://gatb.inria.fr/software/dsk]

• LASTZ [https://github.com/lastz/lastz]

• Tandem Repeats Finder [http://tandem.bu.edu/trf/trf.html]

License

SDquest is distributed under a BSD license. See the LICENSE file for details.

Contacts

Please report any problems directly to the github issue tracker. Also, you can send feedback to lianrong.pu@gmail.com