03_Metagenomes

Bat Shotgun Metagenomic Flow-work

This is the repository for supplementary materials for the upcoming publication

Metagenome-assembled genomes 🧬

Files:

• 📑 03_Lab_journal.ipynb - laboratory journal with commands to reproduce pipeline
• ⚙️ Assembly_pipeline - snakemake pipeline to run metaSPAdes & metaquast
• ⚙️ Filtering_pipeline - snakemake pipeline to filter out short sequences from MAGs using scripts/filter_MAGs.py script
• ⚙️ HUMAnN3_pipeline - snakemake pipeline to run HUMAnN3 on every filtered MAG
• 📁 scripts - folder with miscellaneous scripts used for data analysis:
  • 📝 filter_MAGs.py - script to filter out sequences shorter than 3500 nucleotides from MAGs
  • 📝 abr2tsv.py - script to convert default merged ABRicate output to .tsv format
  • 📝 abr_tsv2presence.py - script to convert ABRicate results from %COVERAGE type to presence/abscence type
  • 📝 filt_humann3.py - script to filter out redundant info from HUMAnN3 outputs
  • 📝 transpose_humann.py - script to transpose HUMAnN3 output & prepare it for input in MaAsLin2
  • 📝 MaAsLin2.R - script to run MaAsLin2 on HUMAnN3 results (it purposely does not uses any normalization method)
  • 📑 ABRicate_visualization_journal.R - laboratory journal to plot ABRicate results as bar-plot and heatmaps
• 📑 HUMAnN3_heatmaps_journal.R - laboratory journal to plot HUMAnN3 results as heatmap (pathway abundance table only)
• 📑 HUMAnN3_volcano_plot_journal.R - laboratory journal to plot MaAsLin2 on HUMAnN3 results as volcano-plots
• 📑 metagenomes.yaml - conda environment

Instruction:

• Create new environment metagenomes

conda env create -f metagenomes.yaml

System

This part of work was done on DSTU's server