ViQUF: De Novo Viral Quasispecies Reconstruction Using Unitig-Based Flow Networks

Freire, Borja; Ladra, Susana; Paramá, José R.; Salmela, Leena

doi:10.1109/tcbb.2022.3190282

Cited by 3 publications

(5 citation statements)

References 31 publications

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“…Since these viruses have high mutation rates due to their RNA-dependent RNA polymerase, haplotypes of viral quasispecies can be highly variable and multiple tools and techniques have been developed to decipher their genetic composition. The methods for haplotype determination and assembly can be differentiated into: (i) reference-based methods that require a previously determined consensus sequence [53,[65][66][67], and (ii) de novo assemblies based on either short-or long-read data [56,[68][69][70][71].…”

Section: Discussionmentioning

confidence: 99%

Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants

Wennmann,

Lim,

Senger

et al. 2024

Journal of General Virology

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Naturally occurring isolates of baculoviruses, such as the Bombyx mori nucleopolyhedrovirus (BmNPV), usually consist of numerous genetically different haplotypes. Deciphering the different haplotypes of such isolates is hampered by the large size of the dsDNA genome, as well as the short read length of next generation sequencing (NGS) techniques that are widely applied for baculovirus isolate characterization. In this study, we addressed this challenge by combining the accuracy of NGS to determine single nucleotide variants (SNVs) as genetic markers with the long read length of Nanopore sequencing technique. This hybrid approach allowed the comprehensive analysis of genetically homogeneous and heterogeneous isolates of BmNPV. Specifically, this allowed the identification of two putative major haplotypes in the heterogeneous isolate BmNPV-Ja by SNV position linkage. SNV positions, which were determined based on NGS data, were linked by the long Nanopore reads in a Position Weight Matrix. Using a modified Expectation–Maximization algorithm, the Nanopore reads were assigned according to the occurrence of variable SNV positions by machine learning. The cohorts of reads were de novo assembled, which led to the identification of BmNPV haplotypes. The method demonstrated the strength of the combined approach of short- and long-read sequencing techniques to decipher the genetic diversity of baculovirus isolates.

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Section: Discussionmentioning

confidence: 99%

Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants

Wennmann,

Lim,

Senger

et al. 2024

Journal of General Virology

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“…Here, the forward read maps to unitig

and the reverse read maps to unitig

. Paired-end information has been used in previous studies for assembling viral quasispecies to untangle assembly graphs ( Freire et al 2023 ). Moreover, paired-end reads are widely used in manual curation steps to join contigs from metagenome assemblies and extend them to longer sequences ( Chen et al 2020 ).…”

Section: Methodsmentioning

confidence: 99%

“…These tools do not resolve the clustered sequences into contiguous genomes and the bins produced often contain a mixture of multiple strains resulting in poor-quality MAGs ( Meyer et al 2022 ). Existing solutions developed for viral quasispecies assembly only consider one species at a time ( Baaijens et al 2020 , Freire et al 2021 , 2023 ) and cannot be applied to complex metagenomes. Despite the recent progress, it is challenging for currently available tools to recover complete high-quality phage genomes from metagenomic data, and a novel approach is required to address this issue.…”

Section: Introductionmentioning

confidence: 99%

Phables: from fragmented assemblies to high-quality bacteriophage genomes

Mallawaarachchi,

Roach,

Decewicz

et al. 2023

Bioinformatics

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Motivation Microbial communities have a profound impact on both human health and various environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of challenges in viral assembly, fragmentation of genomes can occur, and existing tools may recover incomplete genome fragments. Therefore, the identification and characterisation of novel phage genomes remains a challenge, leading to the need of improved approaches for phage genome recovery. Results We introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make. Availability and Implementation Phables is available on GitHub at https://github.com/Vini2/phables.

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“…We also define the confidence of paths ( t → u → v ) termed c p ( t → u → v ) as the number of paired-end reads spanning across unitigs t and u . Paired-end information has been used in previous studies for assembling viral quasispecies (Freire et al 2022; J. Chen, Zhao, and Sun 2018) to untangle assembly graphs.…”

Section: Methodsmentioning

confidence: 99%

“…Moreover, most metagenomic binning tools struggle to distinguish communities of similar viral variants (viral quasispecies), and bins often contain a mixture of multiple strains resulting in poor-quality MAGs (Nissen et al 2021). Existing solutions that are developed to perform viral quasispecies assembly only consider one species at a time (Baaijens, Stougie, and Schönhuth 2020;Freire et al 2021Freire et al , 2022 and cannot be applied to complex metagenomes. Despite the recent progress, it is challenging for currently available tools to recover complete high-quality phage genomes from metagenomic data, and a novel approach is required to address this issue.…”

Section: Introductionmentioning

confidence: 99%

Phables: from fragmented assemblies to high-quality bacteriophage genomes

Mallawaarachchi

Roach

Papudeshi

et al. 2023

Preprint

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Microbial communities found within the human gut have a strong influence on human health. Intestinal bacteria and viruses influence gastrointestinal diseases such as inflammatory bowel disease. Viruses infecting bacteria, known as bacteriophages, play a key role in modulating bacterial communities within the human gut. However, the identification and characterisation of novel bacteriophages remain a challenge. Available tools use similarities between sequences, nucleotide composition, and the presence of viral genes/proteins. Most available tools consider individual contigs to determine whether they are of viral origin. As a result of the challenges in viral assembly, fragmentation of viral genomes can occur, leading to the need for new approaches in viral identification. We introduce Phables, a new computational method to resolve bacteriophage genomes from fragmented viral metagenomic assemblies. Phables identifies bacteriophage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that over 80% of the bacteriophage genomes resolved by Phables have high quality and are longer than the individual contigs identified by existing viral identification tools.

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ViQUF: De Novo Viral Quasispecies Reconstruction Using Unitig-Based Flow Networks

Cited by 3 publications

References 31 publications

Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants

Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants

Phables: from fragmented assemblies to high-quality bacteriophage genomes

Phables: from fragmented assemblies to high-quality bacteriophage genomes

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