Metagenomics_pipeline_bioinformatics

This repository contains PBS job scripts developed for my honours research project focused on metagenomic data analysis. The scripts automate essential steps in processing shotgun sequencing data, including: Quality control of raw sequencing reads using fastp and FastQC Organizing sequencing data and assembly results for streamlined analysis Aligning reads to assembled contigs with BWA and managing alignments with SAMtools Metagenomic binning of genomes using MetaBAT2 Assessing assembly quality with QUAST Summarizing multiple quality control reports via MultiQC All scripts are designed to run efficiently on an HPC cluster with PBS job scheduling, enabling reproducible and scalable data processing. This pipeline supports the project’s goal to characterize microbial communities through metagenomics.