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 phasing
bioRxiv 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 Reads
Journal 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 individuals
Bioinformatics 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 reads
bioRxiv

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 Assembly
Proceedings 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.