Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction

Knyazev, S. P.; Tsyvina, Viachaslau; Shankar, Anupama; Melnyk, Andrew; Artyomenko, Alexander; Malygina, Tatiana; Porozov, Yuri; Campbell, Ellsworth; Mangul, Serghei; Switzer, William M.; Skums, Pavel; Zelikovsky, Alex

doi:10.1101/264242

Cited by 21 publications

(18 citation statements)

References 64 publications

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“…Existing viral quasispecies assemblers include widely evaluated tools like [12,13,14], as well a variety of methods introduced more recently [15,16,17,18,19,20]. These methods can be divided into two classes: reference-guided and reference-free (also referred to as de novo).…”

Section: Introductionmentioning

confidence: 99%

Strain-aware assembly of genomes from mixed samples using flow variation graphs

Baaijens

Stougie

Schönhuth

2019

Preprint

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The goal of haplotype-aware genome assembly is to reconstruct all individual haplotypes from a mixed sample and to provide corresponding abundance estimates. We provide a referencegenome-independent solution based on the construction of a variation graph, capturing all diversity present in the sample. We solve the contig abundance estimation problem and propose a greedy algorithm to efficiently build maximal-length haplotypes. Finally, we obtain accurate frequency estimates for the reconstructed haplotypes through linear programming techniques. Our method outperforms state-of-the-art approaches on viral quasispecies benchmarks and has the potential to assemble bacterial genomes in a strain-aware manner as well.

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Section: Introductionmentioning

confidence: 99%

Strain-aware assembly of genomes from mixed samples using flow variation graphs

Baaijens

Stougie

Schönhuth

2019

Preprint

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“…For example, validation of tools for imputation of cellular and transcriptional heterogeneity should simultaneously evaluate two measures: (i) how close are the reconstructed and true cellular genomic profiles and (ii) how close are reconstructed and true SNV/haplotype frequency distributions. Development of synthetic measures that capture several such characteristics (e.g., based on utilization of earth mover's distance [361]) is highly important.…”

Section: Open Problemsmentioning

confidence: 99%

Eleven grand challenges in single-cell data science

et al. 2020

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The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands-or even millions-of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.

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“…We selected three pipelines (QuRe [10], CliqueSNV [30] and ViQuaS [11]) as an example of suitable programs for viral quasispecies reconstruction and estimation of the frequencies of the haplotypes.…”

Section: Quasispecies Reconstructionmentioning

confidence: 99%

“…Quasispecies reconstruction was performed using QuRe (version 0.99971) [10], CliqueSNV (version 1.4.8) [30] and ViQuaS (version 1.3) [11]. First, we assessed the capability of these programs to reconstruct known quasispecies samples.…”

Section: Inferred Quasispecies For the Four Fmdv Virusesmentioning

confidence: 99%

A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing

Cacciabue

Currá

Carrillo

et al. 2019

Briefings in Bioinformatics

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Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity. However, the analysis of next-generation sequencing data might be challenging for researchers who have never approached the study of viral quasispecies by this methodology. In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data. The guide includes a complete analysis pipeline along with user-friendly descriptions of software and file formats. In addition, we assessed the feasibility of the workf low proposed by analyzing a set of foot-and-mouth disease viruses (FMDV) with different degrees of variability. This guide introduces the analysis of quasispecies of FMDV and other viruses through this kind of approach.

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Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction

Abstract: Highly mutable RNA viruses such as influenza A virus, human immunodeficiency virus and hepatitis C virus exist in infected hosts as highly heterogeneous populations of closely related genomic variants.

Cited by 21 publications

References 64 publications

Strain-aware assembly of genomes from mixed samples using flow variation graphs

Strain-aware assembly of genomes from mixed samples using flow variation graphs

Eleven grand challenges in single-cell data science

A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing

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