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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....
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6524403/ https://www.ncbi.nlm.nih.gov/pubmed/30124794 http://dx.doi.org/10.1093/bioinformatics/bty695 |
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author | Vilsker, Michael Moosa, Yumna Nooij, Sam Fonseca, Vagner Ghysens, Yoika Dumon, Korneel Pauwels, Raf Alcantara, Luiz Carlos Vanden Eynden, Ewout Vandamme, Anne-Mieke Deforche, Koen de Oliveira, Tulio |
author_facet | Vilsker, Michael Moosa, Yumna Nooij, Sam Fonseca, Vagner Ghysens, Yoika Dumon, Korneel Pauwels, Raf Alcantara, Luiz Carlos Vanden Eynden, Ewout Vandamme, Anne-Mieke Deforche, Koen de Oliveira, Tulio |
author_sort | Vilsker, Michael |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6524403 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-65244032019-05-21 Genome Detective: an automated system for virus identification from high-throughput sequencing data Vilsker, Michael Moosa, Yumna Nooij, Sam Fonseca, Vagner Ghysens, Yoika Dumon, Korneel Pauwels, Raf Alcantara, Luiz Carlos Vanden Eynden, Ewout Vandamme, Anne-Mieke Deforche, Koen de Oliveira, Tulio Bioinformatics Applications Notes 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. Oxford University Press 2019-03-01 2018-08-16 /pmc/articles/PMC6524403/ /pubmed/30124794 http://dx.doi.org/10.1093/bioinformatics/bty695 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Vilsker, Michael Moosa, Yumna Nooij, Sam Fonseca, Vagner Ghysens, Yoika Dumon, Korneel Pauwels, Raf Alcantara, Luiz Carlos Vanden Eynden, Ewout Vandamme, Anne-Mieke Deforche, Koen de Oliveira, Tulio Genome Detective: an automated system for virus identification from high-throughput sequencing data |
title | Genome Detective: an automated system for virus identification from high-throughput sequencing data |
title_full | Genome Detective: an automated system for virus identification from high-throughput sequencing data |
title_fullStr | Genome Detective: an automated system for virus identification from high-throughput sequencing data |
title_full_unstemmed | Genome Detective: an automated system for virus identification from high-throughput sequencing data |
title_short | Genome Detective: an automated system for virus identification from high-throughput sequencing data |
title_sort | genome detective: an automated system for virus identification from high-throughput sequencing data |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6524403/ https://www.ncbi.nlm.nih.gov/pubmed/30124794 http://dx.doi.org/10.1093/bioinformatics/bty695 |
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