Genome Assembly of bacterial genome (MRSA)

Summary of MRSA (Methicillin-Resistant Staphylococcus aureus)

Staphylococcus aureus is a Gram-positive, facultative anaerobic bacterium commonly found on human skin and mucous membranes. It is a major cause of hospital- and community-acquired infections. MRSA refers specifically to strains of S. aureus that have acquired resistance to methicillin and other beta-lactam antibiotics, making treatment challenging.

Objectives of the Project

• Run tools to evaluate the quality and quantity of the short reads produced by Illumina MiSeQ.
• Process the output of the quality control tools.
• Improve the quality of the sequencing data.
• Run a tool to assemble a bacterial genome using short reads.
• Run tools to assess the quality of the assemble genome.

Standard Workflow of the Pipeline

• Quality Control (QC)
• Read Trimming
• Genome assembling
• Graph Plotting
• Assembly Inspection

Installation

Install the required softwares. You can manage dependancies using package managers like conda or mamba conda create -n Assembly -c bioconda -c conda-forge fastqc multiqc fastp shovil bandage quast

Usage

1. Quality Control : To assess the quality of the raw short reads.
2. Trimming : To trim adapter and low-quality bases.
3. De Novo Genome Assembly : Shovill
4. Graph Plotting : bandage
5. Assembly Quality Inspection : QUAST

Project Structure

    ├── QC # QC reports generated by FastQC, MultiQc and Trimming using FastP 
    ├──Code # contains bash scripts for each step of the pipeline 
    │ ├── run_fastqc.sh #Script to run fastqc 
    | ├── run.fastp.sh # script to perform read trimming 
    | ├──shovil.sh # script for genome assembly running 
    | ├── quast.sh # script for assembly inspection 
    ├──Assembly Inspection # contains quast reports 
    ├── requirements.txt # list of all the tools utilized in this project 
    ├──Results # contains all the results of the pipeline
    ├── README.md