HapCol: accurate and memory-efficient haplotype assembly from long reads

Bioinformatics
Yuri PirolaPaola Bonizzoni

Abstract

Haplotype assembly is the computational problem of reconstructing haplotypes in diploid organisms and is of fundamental importance for characterizing the effects of single-nucleotide polymorphisms on the expression of phenotypic traits. Haplotype assembly highly benefits from the advent of 'future-generation' sequencing technologies and their capability to produce long reads at increasing coverage. Existing methods are not able to deal with such data in a fully satisfactory way, either because accuracy or performances degrade as read length and sequencing coverage increase or because they are based on restrictive assumptions. By exploiting a feature of future-generation technologies-the uniform distribution of sequencing errors-we designed an exact algorithm, called HapCol, that is exponential in the maximum number of corrections for each single-nucleotide polymorphism position and that minimizes the overall error-correction score. We performed an experimental analysis, comparing HapCol with the current state-of-the-art combinatorial methods both on real and simulated data. On a standard benchmark of real data, we show that HapCol is competitive with state-of-the-art methods, improving the accuracy and the number of phased posi...Continue Reading

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Citations

Jun 10, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Paola BonizzoniSimone Zaccaria
Jun 17, 2016·Bioinformatics·Shilpa GargTobias Marschall
Jan 6, 2017·Nature Protocols·Elaine R Mardis
Nov 22, 2018·Briefings in Functional Genomics·YongKiat WeeMin Zhao
Apr 18, 2019·Bioinformatics·Jasmijn A Baaijens, Alexander Schönhuth
Sep 10, 2020·BMC Genomics·Abishek SankararamanFrançois Baccelli
Jun 5, 2019·Genome Biology·Jana EblerBenedict Paten
Sep 18, 2020·BMC Bioinformatics·Nicola PrezzaGiovanna Rosone
Jun 29, 2018·Bioinformatics·Gryte Satas, Benjamin J Raphael
Oct 23, 2016·Briefings in Bioinformatics·UNKNOWN Computational Pan-Genomics Consortium
Jul 5, 2018·BMC Bioinformatics·Stefano BerettaPaola Bonizzoni
Apr 20, 2019·BMC Bioinformatics·Andrea TangherloniDaniela Besozzi
Feb 12, 2017·BMC Bioinformatics·Andrea BraccialiMassimo Torquati
Oct 29, 2021·Genome Biology·Xiao LuoAlexander Schönhuth

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