Learn Genome Assembly & Annotation In Prokaryote & Eukaryote

Step-by-Step Guide to Assembling and Annotating Eukaryotic and Prokaryotic Genomes

What you'll learn

Understand the biological principles behind genome assembly and annotation

Set up a Linux-based bioinformatics environment, including WSL on Windows

Download and manage raw sequencing data from public repositories like NCBI and ENA

Perform quality control and trimming of sequencing reads using FastQC and porechop

Assemble genomes using SPAdes and Flye

Annotate prokaryotic genomes using Prokka

Annotate Eukaryotic Genomes using AUGUSTUS

Run BLAST for functional annotation and pathway mapping

Predict protein domains and GO terms using HMMER and Pfam databases

Visualize and validate annotation results using Quast

Build reproducible genome assembly and annotation pipelines using Bash scripting

Requirements

Basic understanding of molecular biology and genomics (e.g., DNA structure, gene expression)

Familiarity with command-line tools (Linux/Unix) is helpful but not mandatory — we’ll cover the essentials

A computer with internet access and at least 8 GB RAM (recommended for genome assembly tasks)

Ability to install and run bioinformatics tools (we’ll guide you through setting up WSL or a Linux VM)

Curiosity and willingness to learn hands-on through real datasets and practical exercises

Description

Learn Step by Step Genome Assembly & Annotation in Prokaryotes and EukaryotesTurn raw DNA sequencing data into meaningful biological insights. In this practical, hands-on bioinformatics course, you’ll learn how to perform genome assembly and annotation for both prokaryotic and eukaryotic organisms using real datasets and powerful open-source tools.Whether you’re a student, researcher, or bioinformatics enthusiast, this course will help you master skills used in genomics, biotechnology, medicine, and evolutionary biology. No prior programming experience is required. We start from the basics and guide you through each step.What You’ll LearnPerform quality control and preprocessing of sequencing readsAssemble genomes with tools like SPAdes and FlyeAnnotate genes using Prokka and AUGUSTUSAdd functional data with BLAST and PfamVisualize genomes using QuastBuild reproducible pipelines with Bash scriptingWork confidently with both prokaryotic and eukaryotic datasetsWho This Course Is ForBiology and bioinformatics studentsResearchers and lab techniciansEducators teaching genomics hands-onSelf-learners curious about genome analysisWhat You NeedJust a computer, internet connection, and basic biology knowledge. We’ll guide you through setting up your bioinformatics environment and provide downloadable scripts for practice.By the end of this course, you’ll be able to take raw sequencing reads, assemble a genome, annotate it, visualize results, and prepare them for publication or database submission.Enroll now and start your journey into genome assembly and annotation turning data into discovery.

Overview

Section 1: Course Introduction

Lecture 1 Introduction

Section 2: Linux for Bioinformatics

Lecture 2 Introduction to Linux for Bioinformatics

Lecture 3 Installing Linux or WSL on Windows

Lecture 4 Navigating the Linux File System

Lecture 5 Basic Linux Commands Every Bioinformatician Must Know

Lecture 6 Working with Files: Viewing, Editing, and Processing Genomic Data

Lecture 7 Setting Up Conda and Environment

Section 3: Short Read Genome Assembly and Analysis Using Linux

Lecture 8 Introduction to Genome Assembly Methods & Algorithms

Lecture 9 Overview of Short Read Sequencing Technologies

Lecture 10 Retrieving Short Read Data from Public Repositories

Lecture 11 Installing Tools & Performing Quality Control of Short Reads

Lecture 12 Assembling Short Reads And Visualizing Contigs And Scaffolds

Section 4: Long Read Genome Assembly and Analysis Using Linux

Lecture 13 Introduction to Long Read Sequencing Technologies

Lecture 14 Retrieving Long Read Data & Setting Up the Environment

Lecture 15 Quality Assessment of Long Reads

Lecture 16 Assembling Long Reads into Contigs and Visualizing

Section 5: Prokaryotic Genome Annotation

Lecture 17 Introduction to Genome Annotation

Lecture 18 Prokaryotic Genome Structural Annotation Using Prokka

Lecture 19 Prokaryotic Genome Functional Annotation Using BLAST

Lecture 20 Prokaryotic Genome Domain Prediction Using HMMER

Section 6: Eukaryotic Genome Annotation

Lecture 21 Eukaryotic Genome Structural Annotation

Lecture 22 Eukaryotic Genome Functional Annotation

Biology and bioinformatics students eager to gain hands-on experience in genome assembly and annotation,Early-career researchers looking to analyze sequencing data for their thesis or publications,Educators and mentors who want to integrate practical genomics workflows into their teaching,Lab technicians and data analysts working with NGS data who need reproducible pipelines,Self-learners and enthusiasts curious about how genomes are decoded, assembled, and annotated,Anyone preparing for graduate studies or research roles in genomics, computational biology, or molecular diagnostics