MetaSUB-CMRL

This repository contains the analysis code for the Chennai MetaSUB project. Both R and Python scripts are used for data analysis and plot creation. Please follow the sequence of scripts provided in this README to ensure that the required files are generated for smooth execution.

Python environment setup

• Python = 3.11
• Use requirments.txt to install the required pakages.

Data folder structure

• Chennai_data : data of Chennai samples
• MetaSUB_data.zip : data of MetaSUB (Extract it to folder MetaSUB_data)

Taxonomic classification and comparative analysis of distinct microbial signatures

• code/microbial_signatures_analysis.ipynb

Relative abundance plot

• code/rel_abd_taxa_part_1_taxa_ordering.ipynb
• code/rel_abd_taxa_part_2_barplot.Rmd

species prevalance plot

• code/species_prevalance_plot.Rmd
• results/microbial_signatures/001/Chennai_species_prevalence.csv
• results/microbial_signatures/001/core_species_prevalence.csv

Metagenome-assembled genomes (MAGs) analysis

Here the results of enrichment analysis from Anvi'o tool is further analysed to extract the COG functionalities that are enriched in Chennai MAGs when compared against reference strain from NCBI.

• code/MAG_enrichment_analysis.ipynb
• data/Chennai_data/MAG_enrichment_analysis
• results/MAG_enrichment_analysis

AMR analysis

• code/AMR_analysis.ipynb
• data/Chennai_data/AMR

Microbial diversity and composition across various surface types

• code/Diversity_analysis.Rmd
• code/surface_type_variation_part_1_Maaslin2.Rmd
• code/surface_type_variation_part_2.ipynb
• code/surface_type_variation_part_3_valcano_plot.Rmd

removed samples

368297885 368259717 368258424 368258384 368281370 368257238

sampl_to_remove = ["368297885","368259717", "368258424", "368258384", "368281370", "368257238"]