Virus Metagenomics Classification Pipelines

Overview of virus metagenomics classification pipelines

For virologists working with sequencing data, we have compiled a list of the computational classification workflows published between 2010 and 2017. The list summarises metadata from technical to practical details and lists 51 tools, of which 46 still appear available. The list is meant to inform virologists about the available analysis methods and to help decide which pipeline to use.

Information listed in the overview

The information in the overview is the result of a literature review; we have not yet tested the tools. Moreover, information was gathered from journal publications and, where applicable, from the associated website. Therefore, newer developments may not have been taken into account. This is most strongly the case for pipelines that are under active development and have seen multiple releases since their publication.

The overview is presented as a table with multiple columns describing publication metadata, technical aspects of the pipeline, user friendliness and validating/supporting experiments.

N.B. The “Steps” column lists the order in which different analysis steps are performed by the pipeline: A: assembly , F: filtering, P: pre-processing, Ph: phylogeny, pp: post-processing, S: search.

How to use the table

The table features sorting and filtering options, per column, to narrow down the search to pipelines that best suit your needs. The application columns on the right are probably the most informative to filter first, as these zoom in on your research question. The search can be narrowed down further by selecting required validation, usability or technical features in the other columns. E.g. it is possible to filter pipelines that have been tested several times, that include a graphical user-interface, or that use your favourite sequence search algorithm. Using the link to the tool’s website and the DOI you can see how to use it and read more about its background. A link to the user manual is also included.

The overview was compiled by Sam Nooij, Dennis Schmitz, Harry Vennema, Annelies Kroneman, Matt Cotten, Marion Koopmans

This description was authored by Sam Nooij, PhD candidate at the RIVM (Dutch National Institute for Public Health and the Environment),


Sam Nooij
RIVM (Dutch National Institute for Public Health and the Environment)
16 JULY 2024