Welcome

This repository contains all scripts and data tables used for the analysis of viruses in total metagenomes generated from upland peatland soils in the UK, as presented in Kosmopoulos et al. (2025; in review).

Original, raw sequence reads are deposited to the NCBI Sequence Read Archive under BioProject accession PRJNA1203648. Prokaryotic metagenome-assembled genomes (MAGs) can be accessed from NCBI WGA under accession PRJNA1203648. Viral genomes can be accessed from figshare using the DOI 10.6084/m9.figshare.28107788.

Repository Organization

Scripts contains python and shell scripts used to conduct the analyses and run the tools mentioned in the bioinformatic workflow.

Data contains .RDS formatted data that can be loaded into R for analysis. These data include sample metadata as well as virus and host community summary statistics, virus and hsot genome information, virus and host genome counts, virus-host predictions, gene annotations, read mapping statistics, functional predictions, and more. It also includes the .shp shapefiles used to generate the map in Figure 1A.

Tables include .csv and .tsv formatted data tables used in analyses to generate the data files present in Data. It also contains organized and summarized data that went into the Supplementary Tables.

Notebooks contain R markdown notebooks of all the R code used for the analyses described here. A table of contents for these notebooks is given below.

Plots contain saved plots (PNG formatted) that were generated by the notebooks above, organized into sub-directories by notebook.

Notebook Table of Contents

1. Bioinformatic workflow
2. Gather and organize data
3. Peatland Map and Virus/Host Diversity (Figure 1, Figure S1)
4. Virus Distribution (Figure 2)
5. Virus Genome DESeq and Clustering (Figure S2)
6. Host Genome DESeq and Clustering (Figure S3)
7. Virus and Host Relative Abundance (Figure 3)
8. Virus Genes (Figure 4)
9. Virus-Host Abundance Relationships and Lysogenic Viruses (Figure 5, Figure S4)

James C. Kosmopoulos | kosmopoulos [at] wisc [dot] edu
PhD candidate | Microbiology Doctoral Training Program
Anantharaman lab | anantharamanlab.wisc.edu
Department of Bacteriology | University of Wisconsin - Madison