| Literature DB >> 33532769 |
A Fritz1,2, A Bremges1,2, Z-L Deng1, T-R Lesker1, J Götting2,3, T Ganzenmüller2,3,4, A Sczyrba1,5, A Dilthey6,7, F Klawonn8,9, A C McHardy1,2.
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.Entities:
Year: 2021 PMID： 33532769 PMCID： PMC7852260 DOI： 10.1101/2021.01.25.428049
Source DB: PubMed Journal: bioRxiv