README.md

Bat Shotgun Metagenomic Flow-work

This is the repository for supplementary materials for the upcoming publication

Files:

📑 02_Lab_journal.ipynb - laboratory journal with commands to reproduce pipeline
📁 scripts - folder with miscellaneous scripts used for data analysis:
- 📝 rename_files.py - script to delete _kraken_report files name for convenient data parsing further
- 📝 run_kreport2mpa.sh - script to wrap KrakenTools function kreport2mpa into the cycle to run it on all files in one touch
- 📝 processing_script.py - script to return the 1st row from COMBINED.txt file to counts.txt files & to delete '[X]__' and '_' from organisms names
- 📝 convert2csv.py - script to convert counts.txt files to counts.csv format
- 📝 MaAsLin2.R - script to run MaAsLin2
- 📝 Alpha_div_calculations.R - script to calculate α-diversity
📑 Volcano_plots_journal.R - laboratory journal to plot MaAsLin2 results as a volcano-plot
📑 Bar_plots_journal.R - laboratory journal to plot bar-plots with relative microbial abundance
📑 Alpha_Beta_div_journal.R - laboratory journal to plot α-diversity metrics as box-plots and β-diversity metrics as PCoA plots
📑 diff_an.yaml - conda environment

Instruction:

conda env create -f diff_an.yaml

This part of work was done using: