Foundations in NGS: Genomics | Image

Foundations in NGS: Genomics

Learn to use BASh to analyse any raw NGS dataset from scratch. You will be able to:
  • The standard NGS data preprocessing PIPELINE
  • Prepare dataset for downstream processing by other software
  • Automate your NGS data analysis process
Price: $ 30 $ 20

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I had a great learning experience and importantly, I was super excited today because I got the opportunity to put my learning to use and I was able to do just that!
Aanuoluwa E.A.
Aanuoluwa E.A.
Now in University of Oklahoma

About the Course

About the Course

Fasttrack your data skills in anything NGS. Learn to build and use standard data processing pipelines for various omics datasets; including genomics, RNA-Seq, Chip-Seq, BS-Seq and their variations. You will complete advanced projects in precision medicine, population health and pharmacology

N/B: This does not cover single cell data analysis

Course Syllabus

Welcome to HackBio

  • Welcome to HackBio
  • The New Platform: Learning
  • Testing the Platform
  • Getting Help

Recap on NGS method

  • Welcome to the Exciting World of Next-Generation Sequencing in Genomics!
  • Setting up your PC.
  • Why Bash!
  • Downloading files with wget
  • Managing Folders (Directories)
  • Creating and Reading Files with touch
  • Copy, Paste and Delete
  • Changing Directories
  • Finding Patterns with grep
  • Final Tips and Tricks
  • BASH
  • Introduction to BASh
  • Links and Resources
  • Setup for anaconda for specific tasks/pipelines on Linux (Optional)

NGS Data Pipeline: Quality Control

  • What is Data Preprocessing
  • First thing to do with your sequencing data
  • Performing Quality Control with FastQC
  • Understanding FastQC Reports
  • Aggregating your FastQC Reports for Multiple Datasets
  • MultiQC Usage
  • Using WGET to download our fastQ dataset from GitHub
  • Quality Control
  • Link to resources

NGS Data Pipeline: Trimming

  • Introduction to Data Trimming
  • Trimming off Low Quality Reads
  • Implementing FastP
  • Trimming

NGS Data Pipeline: Genome Mapping

  • Introduction to the Genome Mapping
  • Introduction to Genome Mapping
  • Building Genome Maps: BWA Usage
  • Automating BWA Implementation
  • Genome Mapping
  • Link to resources

Manipulating Your Alignment Map

  • Manipulating Your Alignment Map
  • The Nature of SAM/BAM files
  • Sorting BAM Files
  • SAM vs BAM files: Interconversion and Manipulation
  • Alignment Maps

Handling Bacterial (Haploid) Genomes

  • Variant Calling
  • Implementation for Haploid Genomes
  • Preparing Starting Files and Coding Environment
  • Variant Calling
  • Viewing the result (See next slides to see expected outputs)
  • Expected Results

Project Section

  • Searching for Mutations Leading to Isoniazid Resistance in TB
Technologies you will use

Foundations in NGS: Genomics

100% Practice Oriented
Immediately applicable skills
High quality portfolio projects
Price: $ 30 $ 20

Here is the Plan

Estimated Time

4 weeks

Start by




Real world projects

From industry and academia

Self-paced, flexible learning

Control your learning time and pace

Support for computing

You don't have to buy a new computer to learn

Not sure of where to start?

Take our pathfinder test to get you aligned on passion and future

Your opportunity to land:

βœ… Modern PhD Research Opportunity
βœ… Bioinformatics Scientist/Analyst
βœ… Research Internships