Article

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

2021-01-26

Abstract excerpt

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 v...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: feaedeab-b1a4-52f5-b78d-75cd21fcf940
DOI: 10.1101/2021.01.25.428049

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Haploflow: Strain-resolved <i>de novo</i> assembly of viral genomesDOI 10.1101/2021.01.25.428049Read

Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAsSemantic proximity Read

Strainline: full-length de novo viral haplotype reconstruction from noisy long readsSemantic proximity Read

De novo assembly of viral quasispecies using overlap graphsSemantic proximity Read

Viral quasispecies assembly via maximal clique enumeration.Semantic proximity Read

Viral haplotype reconstruction from long reads with virCHapSemantic proximity Read

VStrains: De Novo Reconstruction of Viral Strains via Iterative Path Extraction From Assembly GraphsSemantic proximity Read

Easing genomic surveillance: A comprehensive performance evaluation of long-read assemblers across multi-strain mixture data of HIV-1 and Other pathogenic viruses for constructing a user-friendly bioinformatic pipelineSemantic proximity Read

De novo haplotype reconstruction in viral quasispecies using paired-end read guided path findingSemantic proximity Read

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations.Semantic proximity Read

De novo assembly of highly diverse viral populationsSemantic proximity Read

Reconstruction of microbial haplotypes by integration of statistical and physical linkage in scaffoldingSemantic proximity Read

Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reductionSemantic proximity Read