Overview of virus metagenomics classification pipelines

Friday 13 Oct 17


Sam Nooij
RIVM (Dutch National Institute for Public Health and the Environment)
COMPARE has compiled a list of virus classification workflows published between 2010 and 2017 with metadata describing their technical aspects, ease-of-use and validating experiments

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.

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.

12 DECEMBER 2018