Genome Detective: An Accurate, Fast and Automated System for Virus Identification from High-throughput next generation sequencing (NGS) data.

Genome Detective is a web-based method to assemble virus genomes from next generation sequencing (NGS) data. Our automated system uses DIAMOND software application with a UniProtRef90 reference dataset to sort reads into viral taxonomy units in buckets. Each taxonomy bucket is assembled idependently using SPAdes and/or metaSPAdes. The produced de novo contigs are joined together in a genome using a novel dynamic programming algorithm, which uses amino-acids and nucleotide scores of all the annotated coding sequences of a reference genome. Genome Detective has been successfully evaluated with synthetic and real clinical datasets of known and unknown viruses. User time is minimal and computational costs are small, allowing the analysis of large NGS and metagenomic datasets.