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

doi:10.1093/bioinformatics/bty695

. 2019 Mar 1;35(5):871-873.

doi: 10.1093/bioinformatics/bty695.

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

Michael Vilsker¹, Yumna Moosa², Sam Nooij³, Vagner Fonseca^{2

4

5}, Yoika Ghysens¹, Korneel Dumon¹, Raf Pauwels¹, Luiz Carlos Alcantara^{4

5

6}, Ewout Vanden Eynden⁷, Anne-Mieke Vandamme^{7

8}, Koen Deforche¹, Tulio de Oliveira²

Affiliations

¹ Emweb bvba, Herent, Belgium.
² KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
³ The Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
⁴ Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
⁵ Laboratory of Hematology Genetic and computational Biology, Goncalo Moniz Research Center, Oswaldo Cruz Foundation (LHGB/CPqGM/FIOCRUZ), Bahia, Brazil.
⁶ Laboratório de Flavivírus, IOC, Fundação Oswaldo Cruz.
⁷ KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.
⁸ Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.

PMID: 30124794
PMCID: PMC6524403
DOI: 10.1093/bioinformatics/bty695

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

Michael Vilsker et al. Bioinformatics. 2019.

. 2019 Mar 1;35(5):871-873.

doi: 10.1093/bioinformatics/bty695.

Authors

Affiliations

¹ Emweb bvba, Herent, Belgium.
² KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
³ The Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
⁴ Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
⁵ Laboratory of Hematology Genetic and computational Biology, Goncalo Moniz Research Center, Oswaldo Cruz Foundation (LHGB/CPqGM/FIOCRUZ), Bahia, Brazil.
⁶ Laboratório de Flavivírus, IOC, Fundação Oswaldo Cruz.
⁷ KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.
⁸ Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.

PMID: 30124794
PMCID: PMC6524403
DOI: 10.1093/bioinformatics/bty695

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.

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References

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[1] Bankevich A. et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 19, 455–477. - PMC - PubMed

[2] Bankevich A. et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 19, 455–477. - PMC - PubMed

[3] Bolger A.M. et al. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120. - PMC - PubMed

[4] Bolger A.M. et al. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120. - PMC - PubMed

[5] Brown J. et al. (2017) FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. Bioinformatics., 33, 3137–3139. - PMC - PubMed

[6] Brown J. et al. (2017) FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. Bioinformatics., 33, 3137–3139. - PMC - PubMed

[7] Buchfink B. et al. (2015) Fast and sensitive protein alignment using DIAMOND. Nat. Methods, 12, 59–60. - PubMed

[8] Buchfink B. et al. (2015) Fast and sensitive protein alignment using DIAMOND. Nat. Methods, 12, 59–60. - PubMed

[9] Conceição-Neto N. et al. (2015) Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Scientific Reports, 5, 16532 Retrieved from 10.1038/srep16532. - DOI - PMC - PubMed

[10] Conceição-Neto N. et al. (2015) Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Scientific Reports, 5, 16532 Retrieved from 10.1038/srep16532. - DOI - PMC - PubMed

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

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

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Abstract

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