A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem.

Bioinformatics
Filippo Geraci

Abstract

Single nucleotide polymorphisms are the most common form of variation in human DNA, and are involved in many research fields, from molecular biology to medical therapy. The technological opportunity to deal with long DNA sequences using shotgun sequencing has raised the problem of fragment recombination. In this regard, Single Individual Haplotyping (SIH) problem has received considerable attention over the past few years. In this article, we survey seven recent approaches to the SIH problem and evaluate them extensively using real human haplotype data from the HapMap project. We also implemented a data generator tailored to the current shotgun sequencing technology that uses haplotypes from the HapMap project. The data we used to compare the algorithms are available on demand, since we think they represent an important benchmark that can be used to easily compare novel algorithmic ideas with the state of the art. Moreover, we had to re-implement six of the algorithms surveyed because the original code was not available to us. Five of these algorithms and the data generator used in this article endowed with a Web interface are available at http://bioalgo.iit.cnr.it/rehap.

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Citations

Sep 17, 2011·Nature Reviews. Genetics·Sharon R Browning, Brian L Browning
Jul 3, 2013·Bioinformatics·Derek Aguiar, Sorin Istrail
Jun 21, 2013·Bioinformatics·Zhi-Zhong ChenLusheng Wang
Jul 19, 2013·Journal of Bioinformatics and Computational Biology·Jingli Wu, Binbin Liang
Jan 11, 2013·BMC Systems Biology·Minzhu XieTao Jiang
Mar 29, 2014·PLoS Computational Biology·Emily BergerBonnie Berger
Nov 3, 2011·PloS One·Francesco StrinoYuval Kluger
Aug 28, 2014·Bioinformatics·Volodymyr Kuleshov
Jan 19, 2012·Journal of Theoretical Biology·Sayyed R Mousavi
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Dec 5, 2014·Genome Medicine·Gustavo GlusmanJared C Roach
Jun 24, 2014·Journal of Theoretical Biology·Xiao ChenTao Xu
Jul 17, 2015·BMC Bioinformatics·Soyeon Ahn, Haris Vikalo
Apr 3, 2012·Journal of Biomedical Informatics·Tai-Chun WangAlbert Y Zomaya
Jun 10, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Paola BonizzoniSimone Zaccaria
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Mar 6, 2013·BMC Genomics·Hirotaka Matsumoto, Hisanori Kiryu
Mar 6, 2018·BMC Bioinformatics·Maryam EtemadiLusheng Wang
Mar 29, 2018·BMC Genomics·Abolfazl HashemiHaris Vikalo
Mar 27, 2019·PloS One·Sina Majidian, Mohammad Hossein Kahaei
May 30, 2020·PLoS Computational Biology·M-Hossein MoeinzadehMartin Vingron
Sep 10, 2020·BMC Genomics·Abishek SankararamanFrançois Baccelli
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Oct 24, 2020·BMC Bioinformatics·Fatemeh ZamaniAlireza Khanteymoori

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Software Mentioned

Fast Hare
PHASE
SpeedHap
HapCUT

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