README

This repository is an R Project used for the analysis of paired viromes and metagenomes as presented in Kosmopoulos et al. (2024).

Original, raw sequence reads representing freshwater, human gut, marine, and soil environments were previously generated. Freshwater reads, originally presented by Tran et al. (2023) and deposited to the JGI Genome Portal under Proposal ID 506328; Marine reads, originally presented by Pesant et al. (2015) and Sunagawa et al. (2015) and deposited to the NCBI Sequence Read Archive under BioProject accessions PRJEB1787 and PRJEB4419; Human gut reads, originally presented by Shkoporov et al. (2019) and deposited to the NCBI Sequence Read Archive under BioProject accession PRJNA545408; Soil, originally presented by Santos-Medellin et al. (2019) and deposited to the NCBI Sequence Read Archive under BioProject accession PRJNA646773.

Repository organization

Data contains .RDS formatted data that can be loaded into R for analysis. These data include sample metadata as well as viral community summary statistics, virus counts, virus-host predictions, gene counts, gene annotations, and read mapping statistics.

Tables include .csv and .tsv formatted data tables used in analyses to generate the data files present in Data.

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. It also contains a notebook workflow.md with commands used for the bioinformatics workflow as described in Figure 1B-C.

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, Table S1
3. Figure 2, Figure S1, Figure S2, Figure S3
4. Figure 3, Figure S4, Figure S5
5. Figure S6
6. Figure 4, Table S2, Table S3, Table S4
7. Figure 5, Table S5, Table S6

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