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Genome Detective: an automated system for virus identification from high-throughput sequencing data.

ABSTRACT: SUMMARY:Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The application uses a novel alignment method that constructs genomes by reference-based linking of de novo contigs by combining amino-acids and nucleotide scores. The software was optimized using synthetic datasets to represent the great diversity of virus genomes. The application was then validated with next generation sequencing data of hundreds of viruses. User time is minimal and it is limited to the time required to upload the data. AVAILABILITY AND IMPLEMENTATION:Available online: http://www.genomedetective.com/app/typingtool/virus/. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Vilsker M

PROVIDER: S-EPMC6524403 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Genome Detective: an automated system for virus identification from high-throughput sequencing data.

Vilsker Michael M Moosa Yumna Y Nooij Sam S Fonseca Vagner V Ghysens Yoika Y Dumon Korneel K Pauwels Raf R Alcantara Luiz Carlos LC Vanden Eynden Ewout E Vandamme Anne-Mieke AM Deforche Koen K de Oliveira Tulio T

Bioinformatics (Oxford, England) 20190301 5

<h4>Summary</h4>Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The application uses a novel alignment method that constructs genomes by reference-based linking of de novo contigs by combining amino-acids and nucleotide scores. The software was optimized using synthetic datasets to represent the great diversity of virus genomes. The application was then validated with next generation sequencing data of hundreds of vi ...[more]

PMID: 30124794

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