How to cite¶
Parts of WhatsHap have been described in different articles. Please choose an appropriate citation depending on your use case.
If you use WhatsHap as a tool:
Marcel Martin, Murray Patterson, Shilpa Garg, Sarah O. Fischer, Nadia Pisanti, Gunnar W. Klau, Alexander Schoenhuth, Tobias Marschall.WhatsHap: fast and accurate read-based phasingbioRxiv 085050doi: 10.1101/085050
To refer to the core WhatsHap phasing algorithm:
Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth.WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing ReadsJournal of Computational Biology, 22(6), pp. 498-509, 2015.
To refer to the pedigree-phasing algorithm and the PedMEC problem:
Shilpa Garg, Marcel Martin, Tobias Marschall.Read-based phasing of related individualsBioinformatics 2016; 32 (12): i234-i242.
WhatsHap’s genotyping algorithm is described here:
Jana Ebler, Marina Haukness, Trevor Pesout, Tobias Marschall, Benedict Paten.Haplotype-aware genotyping from noisy long readsbioRxivdoi: 10.1101/293944
The HapChat algorithm is an alternative MEC solver able to handle higher coverages. It can be used through “whatshap phase –algorithm=hapchat”. It has been described in this paper:
Stefano Beretta, Murray Patterson, Simone Zaccaria, Gianluca Della Vedova, Paola Bonizzoni.HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads.BMC Bioinformatics, 19:252, 2018.
A parallelization of the core dynamic programming algorithm (“pWhatsHap”) has been described in
M. Aldinucci, A. Bracciali, T. Marschall, M. Patterson, N. Pisanti, M. Torquati.High-Performance Haplotype AssemblyProceedings of the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), 245-258, 2015.
pWhatsHap is currently not integrated into the main WhatsHap source code. It is available in branch parallel in the Git repository.
If you use the polyploid phasing algorithm (
whatshap polyphase), please refer to
Sven D. Schrinner, Rebecca Serra Mari, Jana Ebler, Mikko Rautiainen, Lancelot Seillier,Julia J. Reimer, Björn Usadel, Tobias Marschall, Gunnar W. Klau.Haplotype threading: accurate polyploid phasing from long readsGenome Biology