phase genomic variants using DNA sequencing reads
Project description
WhatsHap
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
If you use WhatsHap, please cite:
Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth. WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads. Proceedings of ACM 18th Annual International Conference on Research in Computational Biology (RECOMB), 237-249, 2014. (A self-archived version can be found here)
The version of WhatsHap you find here is the result of further development focused on making the software easy and straightforward to use. WhatsHap is now Open Source software under the MIT license and we welcome contributions.
Parallel Version: pWhatsHap
A parallelization of the core dynamic programming algorithm has been described in
M. Aldinucci, A. Bracciali, T. Marschall, M. Patterson, N. Pisanti, M. Torquati. High-Performance Haplotype Assembly. Proceedings of the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), 245-258, 2015.
The current implementation can be found in branch parallel.
Links
Read the documentation online. Offline documentation is available in the doc/ subdirectory in the repository and in the downloaded tar distribution.
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