Bioinformatics Skill Development Workshop: From Programming to NGS Analysis

A comprehensive workshop designed to take you from Zero Programming to advanced Structural Bioinformatics and Next-Generation Sequencing (NGS) analysis.

• Section I: Data Analysis Using R and R-Studio
• Section II: Python, Biopython, and Molecular Docking
• Section III: Next-Generation Sequencing (NGS) Analysis

Course Overview

Join the next generation of researchers combining Biology, AI, and Innovation. This workshop provides hands-on experience using Linux-based environments and industry-standard bioinformatics tools to solve real-world genomic and structural challenges.

What You Will Learn

Section I: Data Analysis Using R

• Data Wrangling: Import, clean, and reshape real-world datasets using the tidyverse.
• Statistical Analysis: Perform hypothesis testing (t-tests, ANOVA), normality assessments, and post-hoc tests like Tukey HSD and DMRT.
• Visualization: Create publication-ready and interactive plots using ggplot2 and Plotly.
• Multivariate Exploration: Run PCA and cluster analysis for complex biological datasets.

Section II: Python & Structural Bioinformatics

• Programming Foundations: Learn to store, manipulate, and process DNA, RNA, and protein data.
• Biopython Workflows: Automate sequence retrieval from NCBI, perform BLAST searches, and construct phylogenetic trees.
• Structural Analysis: Parse PDB files to analyze hydrophobicity and B-factors, and perform RMSD superimpositions.
• Drug Discovery: Understand the fundamentals of Molecular Docking, ligand preparation, and result interpretation.

Section III: Next-Generation Sequencing (NGS)

• Linux Mastery: Set up and navigate a Linux environment using WSL (Windows Subsystem for Linux).
• Quality Control: Assess raw sequencing data using FastQC and perform read trimming.
• Genome Assembly & Alignment: Assemble reads using SPAdes and align them to reference genomes using BWA and SAMtools.
• Variant Calling: Understand the principles of identifying genetic variations and interpreting VCF files.

Capstone Project

Bring your skills together by performing a complete structural and sequence analysis of a target protein. This includes integrating sequence retrieval, BLAST analysis, structural parsing, and visualization into a single automated workflow.

Key Tools & Packages Covered

• Languages: R, Python, Linux Shell.
• R Packages: dplyr, ggplot2, tidyr, rstatix, car, pheatmap, FactoMineR.
• Python Libraries: Biopython, Pandas, NumPy, Matplotlib.
• NGS Tools: FastQC, SPAdes, BWA, SAMtools.