kongpopjeen/mitogex repository overview

⁠🧬 Mitochondrial Genome Exploration (MitoGEx)

⁠Mitochondrial Genome Explorer: An Integrated Platform for Streamlined Human Mitochondrial Genome Analysis

MitoGEx is a user-friendly tool designed for comprehensive mtDNA analysis, including quality control, alignment, variant calling, annotation, haplogroup classification, and phylogenetic visualization, all in one pipeline.

---

⁠📌 What is it?

MitoGEx is a platform application for mitochondrial DNA analysis.
It integrates:

• Quality control
• Alignment
• Alignment Quality
• Variant calling
• Annotation
• Visualization

Supports WGS and WES.

---

⁠⚙️ How does it work?

MitoGEx automates sequencing data analysis using:

• FastQC, Fastp
• BWA
• GATK Mutect2 (Mitochondrial mode)
• Qualimap 2
• HaploGrep 3
• IQ-TREE 2, Phylocanvas.gl, ETEToolkit

Output includes:

• QC report
• VCFs
• Annotated variants
• Haplogroup classifications
• Phylogenetic trees

For installation, Please go to MitoGEx's github.