About: DisCVR: Rapid viral diagnosis from high-throughput sequencing data

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	DisCVR: Rapid viral diagnosis from high-throughput sequencing data
Creator	Palmarini, Massimo Gunson, Rory Thorburn, Fiona Davison, Andrew Murcia, Pablo Hughes, Joseph Maabar, Maha Vu Cak, Matej
Source	PMC
abstract	High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance, and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample k-mers (twenty-two nucleotide sequences) to k-mers from taxonomically labeled viral genomes. DisCVR was validated using published HTS data for eighty-nine clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method. DisCVR detected human viruses with high sensitivity (79%) and specificity (100%), and was able to detect mixed infections. Moreover, it produced results comparable to those in a published metagenomic analysis of 177 blood samples from patients in Nigeria. DisCVR has been designed as a user-friendly tool for detecting human viruses from HTS data using computers with limited RAM and processing power, and includes a graphical user interface to help users interpret and validate the output. It is written in Java and is publicly available from http://bioinformatics.cvr.ac.uk/discvr.php.
has issue date	2019-08-26(xsd:dateTime)
bibo:doi	10.1093/ve/vez033
bibo:pmid	31528358
has license	cc-by
sha1sum (hex)	471f86c0aa831b75726b025e0b54d623fc1b8479
schema:url	https://doi.org/10.1093/ve/vez033
resource representing a document's title	DisCVR: Rapid viral diagnosis from high-throughput sequencing data
has PubMed Central identifier	PMC6735924
has PubMed identifier	31528358
schema:publication	Virus Evol
resource representing a document's body	covid:471f86c0aa831b75726b025e0b54d623fc1b8479#body_text
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