NGS-SA: Publications and pre-prints of our genomics surveillance work

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

Authors: Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, Vanden Eynden E, Vandamme AM, Deforche K, de Oliveira T

Journal: Bioinformatics, 2019. DOI:


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.


Available online:


Supplementary data are available at Bioinformatics online.