Start using our new user interface: Genome Detective Platform

Genome Detective Virus Tool Version 2.72

May 2023: Genome Detective has been reorganized. Virus identification and subtyping tools remain available on this page, but all analysis starting from FASTQ files have been permanently moved to the new Genome Detective Platform. The Genome Detective Platform supports metagenomic, WGS, amplicon and barcoding analysis of FASTQ files for Virus, Bacteria, Fungi and Parasites (Fungi, Parasites and barcoding (16S/ITS) are available in Beta test upon request). The platform includes long-term data management (storage, retrieval, annotation, search) and intra-sample analysis tools.

The Genome Detective Virus tool (this webpage) offers two functions:

  • The identification of reassembled viral genomes (FASTA files)
  • Virus subtyping tools: phylogenetic genotyping of a reassembled viral genome to obtain the sub-species type. The list of available subtyping tools is at the bottom of this page.
Up to 2000 FASTA sequences may be submitted at once.

Choose type of input file

What kind of input file do you have?
  • FASTQ: The analysis of fastq file for short read (Illumina, IonTorrent, ...) or long read (Oxford Nanopore Technologies, PacBio, ...) has been transferred to the Genome Detective Platform. Please submit your fastq files there.
  • FASTA consensus sequences: You can submit FASTA files below.


Submit one or more FASTA sequences to be typed individually. If you have raw NGS reads (short reads or long reads), please use the Genome Detective Platform to assemble first. Subtyping tools will be linked in the results.
Click here to load some sample data.

click or drop file

Revisit results from a previous run

Available tools

Subtyping tools, identifying subspecies using phylogenetic analysis, are currently available for 20 viruses.

You can submit sequences in FASTA format. To obtain a consensus sequence from a FASTQ file obtained from an NGS sequencer, use the Genome Detective Platform. The Genome Detective Platform will automatically perform a subtyping analysis for the supported viruses.