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Appears in Collections:Computing Science and Mathematics Journal Articles
Peer Review Status: Refereed
Title: PWHATSHAP: efficient haplotyping for future generation sequencing
Author(s): Bracciali, Andrea
Aldinucci, Marco
Patterson, Murray
Marschall, Tobias
Pisanti, Nadia
Merelli, Ivan
Torquati, Massimo
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Keywords: Haplotyping
High-performance computing
Future generation sequencing
Issue Date: 22-Sep-2016
Citation: Bracciali A, Aldinucci M, Patterson M, Marschall T, Pisanti N, Merelli I & Torquati M (2016) PWHATSHAP: efficient haplotyping for future generation sequencing. Nonis A (Editor), Di Serio C (Editor), Lio' P (Editor), Tagliaferri R (Editor) & Rizzo R (Editor) 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2014), Cambridge, UK, 26.06.2014-28.06.2014. BMC Bioinformatics, 17 (Supplement 11).
Abstract: Background: Haplotype phasing is an important problem in the analysis of genomics information. Given a set of DNA fragments of an individual, it consists of determining which one of the possible alleles (alternative forms of a gene) each fragment comes from. Haplotype information is relevant to gene regulation, epigenetics, genome-wide association studies, evolutionary and population studies, and the study of mutations. Haplotyping is currently addressed as an optimisation problem aiming at solutions that minimise, for instance, error correction costs, where costs are a measure of the con dence in the accuracy of the information acquired from DNA sequencing. Solutions have typically an exponential computational complexity. WhatsHap is a recent optimal approach which moves computational complexity from DNA fragment length to fragment overlap, i.e. coverage, and is hence of particular interest when considering sequencing technology's current trends that are producing longer fragments.  Results: Given the potential relevance of ecient haplotyping in several analysis pipelines, we have designed and engineered pWhatsHap, a parallel, high-performance version of WhatsHap. pWhatsHap is embedded in a toolkit developed in Python and supports genomics datasets in standard le formats. Building on WhatsHap, pWhatsHap exhibits the same complexity exploring a number of possible solutions which is exponential in the coverage of the dataset. The parallel implementation on multi-core architectures allows for a relevant reduction of the execution time for haplotyping, while the provided results enjoy the same high accuracy as that provided by WhatsHap, which increases with coverage.  Conclusions: Due to its structure and management of the large datasets, the parallelisation of WhatsHap posed demanding technical challenges, which have been addressed exploiting a high-level parallel programming framework. The result, pWhatsHap, is a freely available toolkit that improves the eciency of the analysis of genomics information.
DOI Link: 10.1186/s12859-016-1170-y
Rights: © The Author(s) 2016 This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver( applies to the data made available in this article, unless otherwise stated.

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