viral_genome_clustering

Here lies the code for taking viral metagenome contigs from human gut microbiomes, analyzing them for completeness, and then clustering the complete genomes

Pipeline:

1. Extract pre-labeled metagenome contigs by country of origin - get_country_contigs.sh
2. Extract phages from pre-labeled metagenome contigs - get_phages.sh
3. Sort phages by length - sort_contigs.py
4. Analyze phage contigs for completeness and lifestyle using CheckV - run_checkv.sh
5. Extract only the complete phage genomes - make_complete_fasta.sh
6. Remove host contamination from genomes using CheckV outputs - cut_complete_genomes.py
7. Create cluster network for complete genomes using Prodigal for ORF calling and vConTACT2 for clustering based on proteins - run_prodigal_vcontact2.sh
8. Edit network node table to include info about our genomes' time periods and lifestyles - annotate_network.py

Analyses:

1. Lifestyle Frequencies by Time Period:
2. Network Colored by Time Period
   • grey = database
   • red = industrial
   • blue = pre-industrial
   • green = paleo

3. Network Colored by Lifestyle
   • grey = database
   • purple = lytic
   • orange = temperate

4. Edge Lengths By Time Period

5. Edge Counts By Time Period

6. Average Neigbor Composition By Time Period

7. Outlier Frequency By Time Period