Repository: Freie Universität Berlin, Math Department

Ranbow: A fast and accurate method for polyploid haplotype reconstruction

Schönhuth, Alexander and Moeinzadeh, M-Hossein and Yang, Jun and Muzychenko, Evgeny and Gallone, Giuseppe and Heller, David and Reinert, Knut and Haas, Stefan and Vingron, Martin (2020) Ranbow: A fast and accurate method for polyploid haplotype reconstruction. PLOS Computational Biology, 16 (5). e1007843. ISSN 1553-7358

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Reconstructing haplotypes from sequencing data is one of the major challenges in genetics. Haplotypes play a crucial role in many analyses, including genome-wide association studies and population genetics. Haplotype reconstruction becomes more difficult for higher numbers of homologous chromosomes, as it is often the case for polyploid plants. This complexity is compounded further by higher heterozygosity, which denotes the frequent presence of variants between haplotypes. We have designed Ranbow, a new tool for haplotype reconstruction of polyploid genome from short read sequencing data. Ranbow integrates all types of small variants in bi- and multi-allelic sites to reconstruct haplotypes. To evaluate Ranbow and currently available competing methods on real data, we have created and released a real gold standard dataset from sweet potato sequencing data. Our evaluations on real and simulated data clearly show Ranbow’s superior performance in terms of accuracy, haplotype length, memory usage, and running time. Specifically, Ranbow is one order of magnitude faster than the next best method. The efficiency and accuracy of Ranbow makes whole genome haplotype reconstruction of complex genome with higher ploidy feasible.

Item Type:Article
Subjects:Mathematical and Computer Sciences > Computer Science
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:2516
Deposited By: Anja Kasseckert
Deposited On:18 Mar 2021 12:48
Last Modified:18 Mar 2021 12:48

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