Learn Genome Assembly & Annotation in Prokaryote & Eukaryote

Name: Learn Genome Assembly & Annotation in Prokaryote & Eukaryote
Rating: 4.0 (9 reviews)

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

Created byRafiq Ur Rehman

Last updated 8/2025

English

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

Course content

6 sections • 22 lectures • 3h 23m total length

Introduction6:13

Introduction to Linux for Bioinformatics9:31
Installing Linux or WSL on Windows13:37
Navigating the Linux File System11:31
Basic Linux Commands Every Bioinformatician Must Know11:00
Working with Files: Viewing, Editing, and Processing Genomic Data13:26
Master viewing, editing, and processing genomic data in Linux with grep, awk, and other text tools to extract fasta headers, filter gff/gtf entries, and count sequences.
Setting Up Conda and Environment4:09

Introduction to Genome Assembly Methods & Algorithms14:42
Overview of Short Read Sequencing Technologies5:20
Retrieving Short Read Data from Public Repositories5:40
Installing Tools & Performing Quality Control of Short Reads10:50
Assembling Short Reads And Visualizing Contigs And Scaffolds12:28
Assemble short reads with spades to produce contigs and scaffolds, and visualize the results with Bandage. Prepare visualization on wsl2/x11 before moving to long-read assembly with flye.
Project 1: Short Read Assembly

Introduction to Long Read Sequencing Technologies8:25
Retrieving Long Read Data & Setting Up the Environment4:02
Download SRA nanopore fastq data and set up a conda environment, then install fly for genome assembly and trimming, perform quality checks, and plan post-assembly validation.
Quality Assessment of Long Reads4:46
Assess long-read quality with fast qc, trim adapters if needed, generate trimmed fastq, and prepare for assembly with fly to produce reliable nanopore-based genome assemblies.
Assembling Long Reads into Contigs and Visualizing6:36
Assemble long Nanopore reads into contigs and visualize the assembly graph with bandage. Explore using the fly tool, review assembly.fasta and gfa outputs, and note about 69 contacts.
Project 2: Long Sequencing Reads Assembly

Introduction to Genome Annotation7:33
Prokaryotic Genome Structural Annotation Using Prokka8:23
Prokaryotic Genome Functional Annotation Using BLAST10:58
Learn how to perform prokaryotic genome functional annotation using blast, build a UniProt blast database, run protein blast against it, and interpret tsv results for gene IDs and protein functions.
Prokaryotic Genome Domain Prediction Using HMMER10:40
Project 3: Prokaryotic Genome Annotation

Eukaryotic Genome Structural Annotation10:48
Annotate eukaryotic genomes with Augustus to predict gene structures and intron and exon boundaries, integrating rna-seq and protein evidence.
Eukaryotic Genome Functional Annotation12:36
Annotate eukaryotic genomes by building a UniProt-based blast database, running Augustus protein queries, predicting domains with hammer against the PFM database, and validating results with quality metrics.
Project 4: Eukaryotic Genome Annotation: Structural and Functional

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 Eukaryotes

Turn 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 Learn

Perform quality control and preprocessing of sequencing reads
Assemble genomes with tools like SPAdes and Flye
Annotate genes using Prokka and AUGUSTUS
Add functional data with BLAST and Pfam
Visualize genomes using Quast
Build reproducible pipelines with Bash scripting
Work confidently with both prokaryotic and eukaryotic datasets

Who This Course Is For

Biology and bioinformatics students
Researchers and lab technicians
Educators teaching genomics hands-on
Self-learners curious about genome analysis

What You Need

Just 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.

Who this course is for:

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

Learn Genome Assembly & Annotation in Prokaryote & Eukaryote

What you'll learn

Explore related topics

Course content

Course Introduction1 lecture • 6min

Linux for Bioinformatics6 lectures • 1hr 3min

Short Read Genome Assembly and Analysis Using Linux5 lectures • 49min

Long Read Genome Assembly and Analysis Using Linux4 lectures • 24min

Prokaryotic Genome Annotation4 lectures • 38min

Eukaryotic Genome Annotation2 lectures • 23min

Requirements

Description

Who this course is for: