ArticlePLoS computational biology2014
Viral quasispecies assembly via maximal clique enumeration.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.GigaScience · 2024Article
- Quasispecies Fitness Partition to Characterize the Molecular Status of a Viral Population. Negative Effect of Early Ribavirin Discontinuation in a Chronically Infected HEV Patient.International journal of molecular sciences · 2022Article
- SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations.Pathogens (Basel, Switzerland) · 2022Article
- The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction.Scientific reports · 2022Article
- Computational graph pangenomics: a tutorial on data structures and their applications.Natural computing · 2022Article
- Strainline: full-length de novo viral haplotype reconstruction from noisy long reads.Genome biology · 2022Article
- Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.Nucleic acids research · 2021Article
- Haploflow: strain-resolved de novo assembly of viral genomes.Genome biology · 2021Article
- Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding.Molecular biology and evolution · 2021Article
- VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples.Patterns (New York, N.Y.) · 2021Article
- Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity.iScience · 2021Article
- Haploflow: Strain-resolvedbioRxiv : the preprint server for biology · 2021Article
- Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.Briefings in bioinformatics · 2021Review
- Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species.Frontiers in microbiology · 2021Article
- Alphaherpesvirus Genomics: Past, Present and Future.Current issues in molecular biology · 2021Review
- Article
- PIQMEE: Bayesian Phylodynamic Method for Analysis of Large Data Sets with Duplicate Sequences.Molecular biology and evolution · 2020Article
- Haplotype threading: accurate polyploid phasing from long reads.Genome biology · 2020Article
- Evaluation of haplotype callers for next-generation sequencing of viruses.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
Corrections and comments
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Virus populations can display high genetic diversity within individual hosts. The intra-host collection of viral haplotypes, called viral quasispecies, is an important determinant of virulence, pathogenesis, and treatment outcome. We present HaploClique, a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples. We develop a statistical model for paired-end reads accounting for mutations, insertions, and deletions. Using an iterative maximal clique enumeration approach, read pairs are assembled into haplotypes of increasing length, eventually enabling global haplotype assembly. The performance of our quasispecies assembly method is assessed on simulated data for varying population characteristics and sequencing technology parameters. Owing to its paired-end handling, HaploClique compares favorably to state-of-the-art haplotype inference methods. It can reconstruct error-free full-length haplotypes from low coverage samples and detect large insertions and deletions at low frequencies. We applied HaploClique to sequencing data derived from a clinical hepatitis C virus population of an infected patient and discovered a novel deletion of length 357±167 bp that was validated by two independent long-read sequencing experiments. HaploClique is available at https://github.com/armintoepfer/haploclique. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2-5.
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