Strainline: full-length de novo viral haplotype reconstruction from noisy long reads

Haplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current methods either can handle only relatively accurate short read data, or collapse haplotype-specific variations into consensus sequence. Here, we present Stra...

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Detalles Bibliográficos
Autores principales: Luo, Xiao, Kang, Xiongbin, Schönhuth, Alexander
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8771625/
https://www.ncbi.nlm.nih.gov/pubmed/35057847
http://dx.doi.org/10.1186/s13059-021-02587-6
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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-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current methods either can handle only relatively accurate short read data, or collapse haplotype-specific variations into consensus sequence. Here, we present Strainline, a novel approach to assemble viral haplotypes from noisy long reads without a reference genome. Strainline is the first approach to provide strain-resolved, full-length de novo assemblies of viral quasispecies from noisy third-generation sequencing data. Benchmarking on simulated and real datasets of varying complexity and diversity confirm this novelty and demonstrate the superiority of Strainline. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-021-02587-6).
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spelling pubmed-87716252022-01-20 Strainline: full-length de novo viral haplotype reconstruction from noisy long reads Luo, Xiao Kang, Xiongbin Schönhuth, Alexander Genome Biol Method Haplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current methods either can handle only relatively accurate short read data, or collapse haplotype-specific variations into consensus sequence. Here, we present Strainline, a novel approach to assemble viral haplotypes from noisy long reads without a reference genome. Strainline is the first approach to provide strain-resolved, full-length de novo assemblies of viral quasispecies from noisy third-generation sequencing data. Benchmarking on simulated and real datasets of varying complexity and diversity confirm this novelty and demonstrate the superiority of Strainline. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-021-02587-6). BioMed Central 2022-01-20 /pmc/articles/PMC8771625/ /pubmed/35057847 http://dx.doi.org/10.1186/s13059-021-02587-6 Text en © The Author(s) 2022 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
Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
title Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
title_full Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
title_fullStr Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
title_full_unstemmed Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
title_short Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
title_sort strainline: full-length de novo viral haplotype reconstruction from noisy long reads
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8771625/
https://www.ncbi.nlm.nih.gov/pubmed/35057847
http://dx.doi.org/10.1186/s13059-021-02587-6
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AT schonhuthalexander strainlinefulllengthdenovoviralhaplotypereconstructionfromnoisylongreads

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