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Updated: Apr 17, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.

Murray Patterson¹, Tobias Marschall^2,3, Nadia Pisanti^4,5

¹1Laboratoire de Biométrie et Biologie Évolutive (LBBE : UMR CNRS 5558), Université de Lyon 1, Villeurbanne, France.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|February 7, 2015

Summary

WhatsHap is a novel haplotype assembly method that optimally phases single nucleotide polymorphisms (SNPs) from sequencing reads. It accounts for longer reads and higher error rates, improving population genetics analyses.

Keywords:

algorithms combinatorial optimization dynamic programming haplotypes next generation sequencing

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Area of Science:

Genomics
Bioinformatics
Population Genetics

Background:

The diploid human genome requires assigning heterozygous single nucleotide polymorphisms (SNPs) to homologous chromosomes.
Haplotypes, or lists of SNPs per chromosome copy, are essential for population genetics.
Current statistical phasing methods do not utilize direct sequencing read information.

Purpose of the Study:

To develop a haplotype assembly approach that can handle increasing sequencing read lengths and error rates.
To provide a method for accurate genome-wide phasing using sequencing data.

Main Methods:

Introduction of WhatsHap, a novel approach for haplotype assembly.
WhatsHap solves the weighted minimum error correction problem, yielding provably optimal solutions.
The method is fixed-parameter tractable (FPT) with sequencing coverage as the parameter.

Main Results:

WhatsHap demonstrates effectiveness with datasets up to 20x coverage.
Approximately 15x coverage is sufficient for reliable phasing of long reads, even with elevated error rates.
WhatsHap achieves favorable switch and flip error rates compared to state-of-the-art statistical phasers.

Conclusions:

WhatsHap is the first approach to optimally address haplotype assembly considering both read length and error rates.
The method provides accurate haplotype phasing crucial for downstream population genetics analyses.
WhatsHap offers a robust solution for current and future sequencing technologies.