Haploflow: strain-resolved de novo assembly of viral genomes

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

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Bibliographic Details
Published inGenome Biology Vol. 22; no. 1; pp. 212 - 19
Main Authors Fritz, Adrian, Bremges, Andreas, Deng, Zhi-Luo, Lesker, Till Robin, Götting, Jasper, Ganzenmueller, Tina, Sczyrba, Alexander, Dilthey, Alexander, Klawonn, Frank, McHardy, Alice Carolyn
Format Journal Article
LanguageEnglish
Published England BioMed Central 19.07.2021
BMC
Subjects
Algorithms
Benchmarking
Contig Mapping - methods
Cytomegalovirus - classification
Cytomegalovirus - genetics
Cytomegalovirus - isolation & purification
Datasets
Error correction & detection
Genome, Viral
Genomes
Haplotypes
High-Throughput Nucleotide Sequencing
Humans
Metagenome
Method
Mutation
Phylogeny
SARS-CoV-2 - classification
SARS-CoV-2 - genetics
SARS-CoV-2 - isolation & purification
Severe acute respiratory syndrome coronavirus 2
Software
Viral infections
Wastewater - virology
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Summary:Abstract With viral infections, multiple related viral strains are often present due to coinfection or within-host evolution. We describe Haploflow, a deBruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm. We assess 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. We show Haploflow reconstructs viral strain genomes from patient HCMV samples and SARS-CoV-2 wastewater samples identical to clinical isolates.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-021-02426-8