MiPoRT (Microbial Profiling of the Respiratory Tract)

MiPoRT study aims to study the microbial profiles and their ecology in the human respiratory tract.

This repository contains code and files to be shared for the research paper titled: 'Pan-microbiome analysis along the human respiratory axis reveals ecological continuum in health and collapse in disease'

Abstract

The MiPoRT (Microbial Profiling of the Respiratory Tract) project integrates over 4,000 metagenomic samples from the human respiratory tract to profile microbial communities across health and disease. This repository hosts the code, workflows, and processed outputs used in the MiPoRT study. Raw sequencing data are archived at ENA under accession PRJEB96845. Supplementary processed data and tables are available via [Add zenodo DOI].

📁 Folder Structure

MiPoRT/
│
├── README.md
├── requirements.txt		# contains list of tools and package used with their versions. Not an exhaustive list.
├── LICENSE
├── .gitignore				# specify which files not to upload
│
├── Data/
│   ├── Raw/				# Raw feature tables of microbial profiles
│   ├── Processed/			# Pre-processed and filtered microbial profiles
│   └── Metadata/			# Sample metadata
│
└──  Scripts/
	├── 01_Preprocessing					# Scripts for preprocessing reads
	├── 02_Diversity_analysis				# Microbiome diversity analysis scripts
	├── 03_Abundance_Prevalence_analysis	# Scripts for plots and stats
	├── 04_Differential_modeling    # Scripts for differential modeling analysis
	└── 05_Source_tracking			# Scripts for source tracking analysis

Note: The scripts in Scripts/ are developed iteratively and are not optimized for general re-use. We provide them for transparency and reproducibility. Only the essential scripts that reproduce key analyses are provided.

Data availability

Raw reads: ENA cite PRJEB96845 . Reused data: List of the BioProjects pulled from ENA/SRA is in Supplementary Table-1.