Reproduction Guide for VirBinn Manuscript

This repository archives the scripts to reproduce the statistical analyses and figures presented in the VirBinn paper.

Processing

The directory processing includes scripts used to preprocess the data:

• genomad.slurm — Runs geNomad for identifying viral signals.
• virsorter2.slurm — Runs VirSorter2 for identifying viral signals.
• combine_viral_ids.sh - Finds viral contigs identified by both geNomad and VirSorter2.
• select_all_viral_contigs.sh — Select out all identified viral contigs.
• generate_mock_contig.sh — Generates the simulated ground-truth assembly by fragmenting high-quality viral contigs and merging them with non-viral host sequences.

Human Gut

The directory hg includes scripts for analyzing and visualizing the results of the human gut dataset:

• heatmap_sim_hg.py — Generates comparative heatmaps of the contact matrix before and after imputation for the top 10 largest ground-truth viral genomes in the simulated human gut dataset.
• before_after_hg.py — Runs Leiden clustering on the raw contact matrix and evaluates bin quality before imputation in the simulated human gut dataset.
• heatmap_hg.py — Generates a heatmap of the contact matrix for the top 10 largest viral bins in the real human gut dataset.
• checkm2_host_hg.sh — Runs CheckM2 to evaluate the host bins in the real human gut dataset.
• checkv_viral_hg.sh — Runs CheckV to evaluate the viral bins after concatenating contigs within each bin in the real human gut dataset.
• range_hg.py — Determines the host range and host taxonomy of high-quality viral bins in the real human gut dataset.

Pig Gut

The directory pig includes scripts for analyzing and visualizing the results of the pig gut dataset:

• heatmap_sim_pig.py — Generates comparative heatmaps of the contact matrix before and after imputation for the top 10 largest ground-truth viral genomes in the simulated pig gut dataset.
• before_after_pig.py — Runs Leiden clustering on the raw contact matrix and evaluates bin quality before imputation in the simulated pig gut dataset.
• heatmap_pig.py — Generates a heatmap of the contact matrix for the top 10 largest viral bins in the real pig gut dataset.
• checkm2_host_pig.sh — Runs CheckM2 to evaluate the host bins in the real pig gut dataset.
• checkv_viral_pig.sh — Runs CheckV to evaluate the viral bins after concatenating contigs within each bin in the real pig gut dataset.
• range_pig.py — Determines the host range and host taxonomy of high-quality viral bins in the real pig gut dataset.

Sheep Gut

The directory sheep includes scripts for analyzing and visualizing the results of the sheep gut dataset:

• heatmap_sim_sheep.py — Generates comparative heatmaps of the contact matrix before and after imputation for the top 10 largest ground-truth viral genomes in the simulated sheep gut dataset.
• before_after_sheep.py — Runs Leiden clustering on the raw contact matrix and evaluates bin quality before imputation in the simulated sheep gut dataset.
• heatmap_sheep.py — Generates a heatmap of the contact matrix for the top 10 largest viral bins in the real sheep gut dataset.
• checkm2_host_sheep.sh — Runs CheckM2 to evaluate the host bins in the real sheep gut dataset.
• checkv_viral_sheep.sh — Runs CheckV to evaluate the viral bins after concatenating contigs within each bin in the real sheep gut dataset.
• range_sheep.py — Determines the host range and host taxonomy of high-quality viral bins in the real sheep gut dataset.

Wastewater

The directory ww includes scripts for analyzing and visualizing the results of the wastewater dataset:

• heatmap_sim_ww.py — Generates comparative heatmaps of the contact matrix before and after imputation for the top 10 largest ground-truth viral genomes in the simulated wastewater dataset.
• before_after_ww.py — Runs Leiden clustering on the raw contact matrix and evaluates bin quality before imputation in the simulated wastewater dataset.
• heatmap_ww.py — Generates a heatmap of the contact matrix for the top 10 largest viral bins in the real wastewater dataset.
• checkm2_host_ww.sh — Runs CheckM2 to evaluate the host bins in the real wastewater dataset.
• checkv_viral_ww.sh — Runs CheckV to evaluate the viral bins after concatenating contigs within each bin in the real wastewater dataset.
• range_ww.py — Determines the host range and host taxonomy of high-quality viral bins in the real wastewater dataset.

Plot

The directory plot includes shared plotting functions:

• before_after.py — Generates heatmaps visualizing the number of viral bins at different completeness levels before and after imputation across all simulated datasets.
• sim_bin.py — Generates stacked bar plots benchmarking VirBinn against other binners in recovering viral bins across all simulated datasets.
• real_bin.py — Generates stacked bar plots benchmarking VirBinn against other binners in recovering viral bins across all real datasets.
• plot_range.py — Generates stacked bar plots visualizing host range and host taxonomy across all real datasets.