Metagenomic Assembly of Human Gut Microbiome

Overview

This project focuses on the assembly and quality assessment of human gut microbiome metagenomic sequencing data. The workflow included raw read quality control, assembly, and evaluation of the resulting contigs using bioinformatics tools. The assembled data provides a foundation for downstream taxonomic profiling and functional annotation.

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Tools Used

• FastQC for initial quality assessment of raw reads.
• SPAdes (MetaSPAdes mode) for metagenomic assembly.
• MetaQUAST for assembly quality evaluation.
• (Optional) BUSCO for assessing genome completeness.

Workflow structure

• Quality Control (QC) of raw reads using FastQC.
• Assembly of high-quality reads into contigs using MetaSPAdes.
• Quality assessment of assemblies using MetaQUAST (and optionally BUSCO).

Projectx/
│── Data/
|── Code   /                # Scripts used for analysis
    ── data_download.sh   # Script to download raw sequencing data
    ── fastqc.sh      # Script to run FastQC
    ── metaspades.sh  # Script to run MetaSPAdes assembly
    ── quast.sh      # Script to run MetaQUAST
    ── busco.sh      # (Optional) Script to run BUSCO
│── QC/                  # FastQC outputs
│── Assembly/            # MetaSPAdes outputs
│── QC/Quast/            # MetaQUAST reports
│── QC/Busco/            # (Optional) BUSCO completeness assessment
│── Report.md            # Full project report
│── Project_overview.md  # Short project overview
│── README.md            # Project documentation