Viral infection diagnostics using high-throughput sequencing

Powerful and tested web-based bioinformatics tools for analyzing and managing your data—from samples to reference genomes.

Boyes, I., Hoffmann, R., and Rott., M. (2020). Virtool: Viral infection diagnostics using next-generation sequencing [Online]. Available online at:

Example of a Pathoscope result hit.

Detect Known Pathogens

Use our fast detection workflow and simple result visualization.

Example of a NuVs result hit.

Detect Novel Pathogens

Use our assembly and profile hidden Markov model workflow to predict novel viral sequences.

The sample management view from Virtool.

Manage sample data

Intuitively manage samples and their analyses.

The quality view for a Virtool sample.


Automatically run and view FastQC-based quality control (QC) on sample data.

The reference list view.

Sequence References

Construct collections of sequences organized into organization taxonomic units (OTU).

The OTU list view for a Virtool reference.

OTU Records

Organize pathogens into organization taxonmic units (OTU), the fundamental building block of references.

The details of a Virtool HMM resource.

Hidden Markov Models

Explore the profile hidden Markov models used to predict novel viral sequences.

The subtractions list view.

Subtraction Genomes

Manage genomes for eliminating non-pathogen reads from analysis workflows.

A collage of citations of bioinformatics tools Virtool makes use of.

Open Source

Virtool is open source and makes heavy use of open source software and published bioinformatic tools.