Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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 Vilsker  1 , Yumna Moosa  2 , Sam Nooij  3 , Vagner Fonseca  2   4   5 , Yoika Ghysens  1 , Korneel Dumon  1 , Raf Pauwels  1 , Luiz Carlos Alcantara  4   5   6 , Ewout Vanden Eynden  7 , Anne-Mieke Vandamme  7   8 , Koen Deforche  1 , Tulio de Oliveira  2
Affiliations

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

Michael Vilsker et al. Bioinformatics. .

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.

PubMed Disclaimer

References

    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
    1. Bolger A.M. et al. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120. - PMC - PubMed
    1. 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
    1. Buchfink B. et al. (2015) Fast and sensitive protein alignment using DIAMOND. Nat. Methods, 12, 59–60. - PubMed
    1. 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

Publication types