Genome binning of viral entities from bulk metagenomics data - HQ virus genomes

Affiliations

1 Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark

2 Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA

3 Statens Serum Institut, Viral & Microbial Special diagnostics, Copenhagen, Denmark

4 National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark

5 Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark

6 Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark

7 Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark

This upload is related to: 
https://zenodo.org/record/5821973#.YhNojKpKhTY 

Manuscript: https://www.nature.com/articles/s41467-022-28581-5 

Methods description

Binned viral genomes, also sometimes referred to as viral MAGs (vMAGs), were mined from bulk metagenomics dataset in the paper including COPSAC (n=662) and HMP2 (n=1317).

The binned viruses were parsed with CheckV (Nayfach et al. 2021) to establish viral completeness and overall quality. 

Here we upload the following for COPSAC and HMP2 datasets:

- CheckV quality summary for HQ viruses

- Sequences of binned HQ viruses