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.
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