Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data.

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

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

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2018-10-24T16:33:26Z No. of bitstreams: 1 Vilsker M Genome...2018.pdf: 188021 bytes, checksum: 6e033cec3fa3935db76c651a7ee16c6f (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2018-10-24T17:02:13Z (GMT) No. of bitstreams: 1 Vilsker M Genome...2018.pdf: 188021 bytes, checksum: 6e033cec3fa3935db76c651a7ee16c6f (MD5)Made available in DSpace on 2018-10-24T17:02:13Z (GMT). No. of bitstreams: 1 Vilsker M Genome...2018.pdf: 188021 bytes, checksum: 6e033cec3fa3935db76c651a7ee16c6f (MD5) Previous issue date: 2018South African Medical Research Council (MRC-RFA-UFSP-01-2013/UKZN HIVEPI), a Royal Society Newton Advanced Fellowship (TdO), the VIROGENESIS project receives funding from the European Union’s Horizon 2020 Research and Innovation Program (under Grant Agreement no. 634650) and the National Institutes of Health Common Fund, grant number U24HG006941Emweb bvba. Herent, Belgium.University of KwaZulu-Natal. School of Laboratory Medicine and Medical Sciences. Nelson R Mandela School of Medicine. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa.The Dutch National Institute for Public Health and the Environment. Bilthoven, The Netherlands.University of KwaZulu-Natal. School of Laboratory Medicine and Medical Sciences. Nelson R Mandela School of Medicine. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa / Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Belo Horizonte, MG, Brasil / Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Hematologia, Genética e Biologia Computacional. Salvador, BA, Brasil.Emweb bvba. Herent, Belgium.Emweb bvba. Herent, Belgium.Emweb bvba. Herent, Belgium.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Belo Horizonte, MG, Brasil / Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Hematologia, Genética e Biologia Computacional. Salvador, BA, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil.Rega Institute for Medical Research. KU Leuven. Department of Microbiology and Immunology. Clinical and Epidemiological Virology. Leuven, Belgium.Rega Institute for Medical Research. KU Leuven. Department of Microbiology and Immunology. Clinical and Epidemiological Virology. Leuven, Belgium / Universidade Nova de Lisboa. Instituto de Higiene e Medicina Tropical. Health and Tropical Medicine. Unidade de Microbiologia. Lisbon, Portugal.Emweb bvba. Herent, Belgium.University of KwaZulu-Natal. School of Laboratory Medicine and Medical Sciences. Nelson R Mandela School of Medicine. College of Health Sciences. KwaZulu-Natal Research Innovation and Sequencing Platform. Durban, South Africa.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

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

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.status: publishe