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Haploflow: Strain-resolved de novo assembly of viral genomes.

ABSTRACT: 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.

SUBMITTER: Fritz A

PROVIDER: S-EPMC7852260 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Haploflow: Strain-resolved <i>de novo</i> assembly of viral genomes.

Fritz A A Bremges A A Deng Z-L ZL Lesker T-R TR Götting J J Ganzenmüller T T Sczyrba A A Dilthey A A Klawonn F F McHardy A C AC

bioRxiv : the preprint server for biology 20210126

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 <i>de novo</i> 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 rec ...[more]

PMID: 33532769

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Haploflow: strain-resolved de novo assembly of viral genomes.

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