• Workflows Major processing steps writtein Widdle-scripts/workflows can be found in wdls directory. Pipelines/wdls used in this repository for data processing can be imported into a relevant environment like Terra (https://firecloud.terra.bio/#).
• Workflow scripts Relevant individual R and python scripts related to every workflow can be found in code directory

Virus genomes and annotation have been deposited on Zenondo DOI: https://zenodo.org/record/6579480#.Yo3xHZNBweY

If you find any of the supporting code or information useful, please remember to cite the following articles:

• https://www.nature.com/articles/s41564-023-01370-6 (PMID: 37188814)

And S. Nayfach et al. for relevant code for organising viruses into vOTUs and genus-level groups.

• https://www.nature.com/articles/s41564-021-00928-6 (PMID: 34168315)