Haploflow: Strain-resolvedde novoassembly 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.

Critical Assessment of Metagenome Interpretation - the second round of challenges

“…Assemblies were evaluated with MetaQUAST v.5.1.0rc 37 , which was adapted for the evaluation of strain-resolved assembly (Supplementary text). To test the ability of the assemblers to generate near-complete strain-resolved genomes, we determined strain recall and precision, similar to 38 (Supplementary Table 3). Strain recall measures how many genomes are recovered with high genome fraction and few mismatches (mm).…”

“…Finally, the number of misassemblies describes the number of contigs which either contain a gap of more than 1kb, contain inserts of more than 1kb or align to different genomes. In addition to these metrics, we determined the strain recall and strain precision, similar to 38 , to quantify the presence of high-quality, strain-resolved assemblies. Strain recall is defined as the fraction of highquality (more than 90% genome fraction and less than 100 mismatches per 100 kb) genome assemblies recovered for all ground truth genomes.…”

Haploflow: strain-resolved de novo assembly of viral genomes

“…The code of Haploflow is available with a GPLv3 license on Github under https://github.com/hzi-bifo/Haploflow [78]. The version (v0.2) used for the assemblies in this publication is available under the DOI https://doi.org/10.5281/zenodo.…”

Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics

“…As a common limitation among all nanopore sequencing kits, high sequencing error rates limit the accurate characterization of quasi-species, new strains or subtypes of a virus and de novo assembly of viral reads [46,59,60]. In a given infected plant, closely related viral strains can be present with high average nucleotide identity (NI), and the assembly of individual strains present in low abundance or with low variation is complicated and challenging [61,62]. Even so, the capability of direct RNA sequencing kit for identifying viral strains with 20% to 40% divergence in term of NI has been demonstrated [63].…”

“…Even so, the capability of direct RNA sequencing kit for identifying viral strains with 20% to 40% divergence in term of NI has been demonstrated [63]. In addition, Haploflow, a new strain-resolving assembler, has been described, which considers the differential coverage between strains to deconvolute the assembly graph into strain resolved genome assemblies and has been used to reconstruct viral strain genomes from human cytomegalovirus positive samples and SARS-CoV-2 wastewater samples [61]. Also, using the full reference sequence of the virus and a BLAST search with phylogeny is recommended for viral phylogeny and viral variation studies [60].…”