04_Densoviruses

Bat Shotgun Metagenomic Flow-work

This is the repository for supplementary materials for the upcoming publication

Densoviruses 🦠

Files:

• 📑 04_Lab_journal.ipynb - laboratory journal with commands to reproduce pipeline
• ⚙️ VirExtr_pipeline - snakemake pipeline to extract densoviral sequences from MAGs using custom BLAST database, scripts/extract_seqs.py script and VirSorter2
• ⚙️ GA_pipeline - snakemake pipeline to annotate densoviral genomes using prokka
• 📁 scripts - folder with miscellaneous scripts used for data analysis:
  • 📝 extract_seqs.py - script to extract longest alignment sequences according to BLAST results from filtered MAGs
  • 📝 rename_seqs.py - script to rename sequences from >NODE_632_length_4705_cov_657475.178280 to Densovirinae_sp._isolate_RBHC_VM_# etc.
  • 📝 add_space_gbk.py - script that fixes prokka output by adding space between seq name and seq length making it eligable for input in Proksee
  • 📝 midpoint_root.py - script to root phylogenetic tree at mid point
• 📁 BLAST_vs_Densoviruses - folder with BLAST outputs of running filtered MAGs against custom BLAST database containing densoviruses complete genomes from RefSeq
• 📑 denso.yaml - conda environment
• 📑 vs2.yaml - conda environment

Instruction:

• Create new environment denso

conda env create -f denso.yaml

• Create new environment vs2

conda env create -f vs2.yaml

For running lab journal use denso.yaml environment. vs2.yaml environment will be automatically used when running VirExtr_pipeline snakemake pipeline

System

This part of work was done using:

• OS: Ubuntu 22.04 (WSL2 on Windows 11 22H2)
• RAM: 32GB (16 for WSL2)
• CPU: Intel Xeon E5-2670v3