About: A binning tool to reconstruct viral haplotypes from assembled contigs

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About: A binning tool to reconstruct viral haplotypes from assembled contigs Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	A binning tool to reconstruct viral haplotypes from assembled contigs
Creator	Chen, Jiao Shang, Jiayu Sun, Yanni Wang, Jianrong
Source	BioRxiv; MedRxiv
abstract	Infections by RNA viruses such as Influenza, HIV still pose a serious threat to human health despite extensive research on viral diseases. One challenge for producing effective prevention and treatment strategies is high intra-species genetic diversity. As different strains may have different biological properties, characterizing the genetic diversity is thus important to vaccine and drug design. Next-generation sequencing technology enables comprehensive characterization of both known and novel strains and has been widely adopted for sequencing viral populations. However, genome-scale reconstruction of haplotypes is still a challenging problem. In particular, haplotype assembly programs often produce contigs rather than full genomes. As a mutation in one gene can mask the phenotypic effects of a mutation at another locus, clustering these contigs into genome-scale haplotypes is still needed. We developed a contig binning tool, VirBin, which clusters contigs into different groups so that each group represents a haplotype. Commonly used features based on sequence composition and contig coverage cannot effectively distinguish viral haplotypes because of their high sequence similarity and heterogeneous sequencing coverage for RNA viruses. VirBin applied prototype-based clustering to cluster regions that are more likely to contain mutations specific to a haplotype. The tool was tested on multiple simulated sequencing data with different haplotype abundance distributions and contig sizes, and also on mock quasispecies sequencing data. The benchmark results with other contig binning tools demonstrated the superior sensitivity and precision of VirBin in contig binning for viral haplotype reconstruction. https://github.com/chjiao/VirBin yannisun@cityu.edu.hk
has issue date	2019-07-16(xsd:dateTime)
bibo:doi	10.1101/704288
has license	medrxiv
sha1sum (hex)	4c35605124dd8011395240fac71e80b52ddbbe7e
schema:url	https://doi.org/10.1101/704288
resource representing a document's title	A binning tool to reconstruct viral haplotypes from assembled contigs
schema:publication	bioRxiv
resource representing a document's body	covid:4c35605124dd8011395240fac71e80b52ddbbe7e#body_text
is schema:about of	named entity 'BINNING' named entity 'RECONSTRUCT' named entity 'BIOLOGICAL PROPERTIES' named entity 'GENETIC DIVERSITY' covid:arg/4c35605124dd8011395240fac71e80b52ddbbe7e named entity 'BENCHMARK' named entity 'MOCK' named entity 'TOOL' named entity 'DISTRIBUTIONS' named entity 'GENE' named entity 'REGIONS' named entity 'VACCINE' named entity 'NOVEL' named entity 'TOOL' named entity 'VIRAL' named entity 'HAPLOTYPES' named entity 'SPECIES' named entity 'KNOWN' named entity 'GROUPS' named entity 'CLUSTERING' named entity 'PRECISION' named entity 'USED' named entity 'INTRA' named entity 'LIKELY' named entity 'QUASISPECIES' named entity 'CLUSTER' named entity 'APPLIED' named entity 'CHARACTERIZATION' named entity 'GROUP' named entity 'HAPLOTYPE RECONSTRUCTION' named entity 'STRATEGIES' named entity 'TREATMENT' named entity 'EXTENSIVE' named entity 'CONTIGS' named entity 'PREVENTION' named entity 'PROGRAMS' named entity 'RNA VIRUSES' named entity 'COVERAGE' named entity 'POPULATIONS' named entity 'PRODUCING' named entity 'EFFECTS' named entity 'LOCUS' named entity 'HAPLOTYPES' named entity 'HIV' named entity 'COM' named entity 'SPECIFIC' named entity 'IMPORTANT' named entity 'INFLUENZA' named entity 'TOOLS' named entity 'ABUNDANCE' named entity 'RESULTS' named entity 'CONTIGS' named entity 'HIGH' named entity 'RATHER' named entity 'HAPLOTYPE' named entity 'SIZES' named entity 'TO CONTAIN' named entity 'EFFECTIVE' named entity 'ENABLES' named entity 'MULTIPLE' named entity 'SEQUENCE COMPOSITION' named entity 'SENSITIVITY' named entity 'MUTATIONS' named entity 'SEQUENCING DATA' named entity 'STRAINS' named entity 'MASK' named entity 'SEQUENCING' named entity 'PROTOTYPE' named entity 'BASED' named entity 'DIFFERENT' named entity 'PRODUCE' named entity 'CONTIG' named entity 'BINNING' named entity 'PROBLEM' named entity 'POSE' named entity 'ASSEMBLY' named entity 'SCALE' named entity 'INFECTIONS' named entity 'HUMAN HEALTH' named entity 'VIRAL' named entity 'EDU'

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