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Haploflow: Strain-resolved de novo assembly of viral genomes

In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm. We assessed Haploflow acr...

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Autores principales: Fritz, A., Bremges, A., Deng, Z.-L., Lesker, T.-R., Götting, J., Ganzenmüller, T., Sczyrba, A., Dilthey, A., Klawonn, F., McHardy, A.C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7852260/
https://www.ncbi.nlm.nih.gov/pubmed/33532769
http://dx.doi.org/10.1101/2021.01.25.428049
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author Fritz, A.
Bremges, A.
Deng, Z.-L.
Lesker, T.-R.
Götting, J.
Ganzenmüller, T.
Sczyrba, A.
Dilthey, A.
Klawonn, F.
McHardy, A.C.
author_facet Fritz, A.
Bremges, A.
Deng, Z.-L.
Lesker, T.-R.
Götting, J.
Ganzenmüller, T.
Sczyrba, A.
Dilthey, A.
Klawonn, F.
McHardy, A.C.
author_sort Fritz, A.
collection PubMed
description In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm. We assessed Haploflow across multiple benchmark data sets of increasing complexity, showing that Haploflow is faster and more accurate than viral haplotype assemblers and generic metagenome assemblers not aiming to reconstruct strains. Haplotype reconstructed high-quality strain-resolved assemblies from clinical HCMV samples and SARS-CoV-2 genomes from wastewater metagenomes identical to genomes from clinical isolates.
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spelling pubmed-78522602021-02-03 Haploflow: Strain-resolved de novo assembly of viral genomes Fritz, A. Bremges, A. Deng, Z.-L. Lesker, T.-R. Götting, J. Ganzenmüller, T. Sczyrba, A. Dilthey, A. Klawonn, F. McHardy, A.C. bioRxiv Article In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm. We assessed Haploflow across multiple benchmark data sets of increasing complexity, showing that Haploflow is faster and more accurate than viral haplotype assemblers and generic metagenome assemblers not aiming to reconstruct strains. Haplotype reconstructed high-quality strain-resolved assemblies from clinical HCMV samples and SARS-CoV-2 genomes from wastewater metagenomes identical to genomes from clinical isolates. Cold Spring Harbor Laboratory 2021-01-26 /pmc/articles/PMC7852260/ /pubmed/33532769 http://dx.doi.org/10.1101/2021.01.25.428049 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Fritz, A.
Bremges, A.
Deng, Z.-L.
Lesker, T.-R.
Götting, J.
Ganzenmüller, T.
Sczyrba, A.
Dilthey, A.
Klawonn, F.
McHardy, A.C.
Haploflow: Strain-resolved de novo assembly of viral genomes
title Haploflow: Strain-resolved de novo assembly of viral genomes
title_full Haploflow: Strain-resolved de novo assembly of viral genomes
title_fullStr Haploflow: Strain-resolved de novo assembly of viral genomes
title_full_unstemmed Haploflow: Strain-resolved de novo assembly of viral genomes
title_short Haploflow: Strain-resolved de novo assembly of viral genomes
title_sort haploflow: strain-resolved de novo assembly of viral genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7852260/
https://www.ncbi.nlm.nih.gov/pubmed/33532769
http://dx.doi.org/10.1101/2021.01.25.428049
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