This repository contains the pipeline for analyzing metagenomic data from environmental samples using various bioinformatics tools on a Linux system. The project involves quality control, read trimming, assembly, binning, taxonomic profiling, and visualization using open-source tools like FastQC, Trimmomatic, SPAdes, MaxBin, Kraken2, and Krona.
data/raw_data/: Contains the raw data downloaded from NCBI repository.
data/working_data/: Contains intermediate data (inside different subdirectories) produced in downstream analyses.
metadata/: Information of samples, reference paper, etc
results/: Includes final visualizations, such as abundance plots, apha diversity plots, etc.
scripts/: Markdown files for the analysis.
docs/: Documentation of the work and landing page for the project website.