nPhase: an accurate and contiguous phasing method for polyploids

While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short rea...

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Autores principales: Abou Saada, Omar, Tsouris, Andreas, Eberlein, Chris, Friedrich, Anne, Schacherer, Joseph
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082856/
https://www.ncbi.nlm.nih.gov/pubmed/33926549
http://dx.doi.org/10.1186/s13059-021-02342-x
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author Abou Saada, Omar
Tsouris, Andreas
Eberlein, Chris
Friedrich, Anne
Schacherer, Joseph
author_facet Abou Saada, Omar
Tsouris, Andreas
Eberlein, Chris
Friedrich, Anne
Schacherer, Joseph
author_sort Abou Saada, Omar
collection PubMed
description While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy (https://github.com/OmarOakheart/nPhase). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of each chromosome (heterozygosity rate ≥ 0.5%). nPhase allows population genomics and hybrid studies of polyploids. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02342-x.
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spelling pubmed-80828562021-04-29 nPhase: an accurate and contiguous phasing method for polyploids Abou Saada, Omar Tsouris, Andreas Eberlein, Chris Friedrich, Anne Schacherer, Joseph Genome Biol Method While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy (https://github.com/OmarOakheart/nPhase). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of each chromosome (heterozygosity rate ≥ 0.5%). nPhase allows population genomics and hybrid studies of polyploids. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02342-x. BioMed Central 2021-04-29 /pmc/articles/PMC8082856/ /pubmed/33926549 http://dx.doi.org/10.1186/s13059-021-02342-x Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Abou Saada, Omar
Tsouris, Andreas
Eberlein, Chris
Friedrich, Anne
Schacherer, Joseph
nPhase: an accurate and contiguous phasing method for polyploids
title nPhase: an accurate and contiguous phasing method for polyploids
title_full nPhase: an accurate and contiguous phasing method for polyploids
title_fullStr nPhase: an accurate and contiguous phasing method for polyploids
title_full_unstemmed nPhase: an accurate and contiguous phasing method for polyploids
title_short nPhase: an accurate and contiguous phasing method for polyploids
title_sort nphase: an accurate and contiguous phasing method for polyploids
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082856/
https://www.ncbi.nlm.nih.gov/pubmed/33926549
http://dx.doi.org/10.1186/s13059-021-02342-x
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