Supporting code for manuscript:

"dsRNA-based viromics: A novel tool unveiled the hidden soil viral communities"

This github repository contains the following files:

1- Taxonomy Extraction: Extract taxonomy information for IMG/VR Blast result

2- Prepare data for analysis in R: Manipulate and prepare necessary data and tables to plot taxonomy results

3- Plotting Stacked Bar Charts and HeatMaps: Creates two functions that generate stacked bar chart and heatmaps for each taxonomic level

4- Diversity Indices Calculation: Calculates richness and diversity indices (Shannon and Simpson) for each taxonomic level and Violin Plot

5- Beta diversity and PCoA: Calculate Bray-Curtis dissimilarity matrix and PCoA plot

Folders:

1- Abundance_dir: This folder contains the abundance results of the SOVAP pipeline for all datasets

2- RdRp_dir: This folder contains the RdRp Sequences from all datasets

• 2.1- RdRp-Scan_dir: This folder contains the RdRp Analysis Results with RdRp-Scan approach: alignments and Newick files
• 2.2- WSH_dir: This folder contains the RdRp Analysis Results with WSH approach: alignments and Newick files

3- Plasmid_dir: This folder contains the plasmid results of the geNomad tool for all datasets (final.contigs_plasmid_summary.tsv)

4- Virus_dir: This folder contains the virus results of the geNomad tool for all datasets (final.contigs_virus_summary.tsv)

If you have any other questions or concerns related to the code or analysis, please create a new issue on Github.

If you find this code helpful, please cite:

• Manuscript DOI
• Poursalavati A. (2023). SOVAP v.1.3 : Soil Virome Analysis Pipeline (1.3). Zenodo. https://doi.org/10.5281/zenodo.7700081