phasebook: haplotype-aware de novo assembly of diploid genomes from long reads

Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies have greatly improved genome assembly. However, current long-read assemblers are either reference based, so introduce biases, or fail to capture the haplo...

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Autores principales: Luo, Xiao, Kang, Xiongbin, Schönhuth, Alexander
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8549298/
https://www.ncbi.nlm.nih.gov/pubmed/34706745
http://dx.doi.org/10.1186/s13059-021-02512-x
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author Luo, Xiao
Kang, Xiongbin
Schönhuth, Alexander
author_facet Luo, Xiao
Kang, Xiongbin
Schönhuth, Alexander
author_sort Luo, Xiao
collection PubMed
description Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies have greatly improved genome assembly. However, current long-read assemblers are either reference based, so introduce biases, or fail to capture the haplotype diversity of diploid genomes. We present phasebook, a de novo approach for reconstructing the haplotypes of diploid genomes from long reads. phasebook outperforms other approaches in terms of haplotype coverage by large margins, in addition to achieving competitive performance in terms of assembly errors and assembly contiguity. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-021-02512-x).
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spelling pubmed-85492982021-10-27 phasebook: haplotype-aware de novo assembly of diploid genomes from long reads Luo, Xiao Kang, Xiongbin Schönhuth, Alexander Genome Biol Method Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies have greatly improved genome assembly. However, current long-read assemblers are either reference based, so introduce biases, or fail to capture the haplotype diversity of diploid genomes. We present phasebook, a de novo approach for reconstructing the haplotypes of diploid genomes from long reads. phasebook outperforms other approaches in terms of haplotype coverage by large margins, in addition to achieving competitive performance in terms of assembly errors and assembly contiguity. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-021-02512-x). BioMed Central 2021-10-27 /pmc/articles/PMC8549298/ /pubmed/34706745 http://dx.doi.org/10.1186/s13059-021-02512-x Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This 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
Luo, Xiao
Kang, Xiongbin
Schönhuth, Alexander
phasebook: haplotype-aware de novo assembly of diploid genomes from long reads
title phasebook: haplotype-aware de novo assembly of diploid genomes from long reads
title_full phasebook: haplotype-aware de novo assembly of diploid genomes from long reads
title_fullStr phasebook: haplotype-aware de novo assembly of diploid genomes from long reads
title_full_unstemmed phasebook: haplotype-aware de novo assembly of diploid genomes from long reads
title_short phasebook: haplotype-aware de novo assembly of diploid genomes from long reads
title_sort phasebook: haplotype-aware de novo assembly of diploid genomes from long reads
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8549298/
https://www.ncbi.nlm.nih.gov/pubmed/34706745
http://dx.doi.org/10.1186/s13059-021-02512-x
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