Bacterial Whole Genome Sequence Analysis

Authors

Tahsin Khan, MPhil, MS

Naimul Islam Faysal, MSc

Tazkia Ahmed, MSc

Tanzim Rahman, MSc

Published

June 11, 2026

Overview

This course is designed for beginners who want to analyse whole genome sequencing data from bacterial isolates. Throughout the course we will introduce tools that are commonly used and basic requirements for analyzing any bacterial genome. Along the way, we will teach you the foundational bioinformatic skills

TipLearning Objectives

By the end of this course, participants should be able to:

  • understand what the main technologies used for high throughput sequencing are
  • use the unix command line to navigate a filesystem, manipulate files, launch programs and write scripts for reproducible analysis
  • recognize the structure of common sequence file formats
  • run basic quality control of samples
  • assemble the reads to construct contigs or scaffolds of the genome
  • check the quality and completeness of the contigs
  • classify taxonomy of that organism
  • annotate the genome to identify coding DNA sequences and proteins
  • identify core genes and construct phylogenetic tree
  • investigate pathogen transmission dynamics

Target audience

This course is primarily aimed at public health officials including doctors, lab workers and clinicians who work with bacterial diseases and would like to get started in using genomic and bioinformatics approaches for the surveillance of their causative bacterial pathogens. We assume little or no prior experience in bioinformatics.

Prerequisites

people who have

  1. Personal computer or laptop
    • RAM: 16GB
    • CPU: 8 Core
    • Windows/Linux/Mac OS
  2. Familiarity with R and Bash

Authors

about the authors:

  • Tahsin Khan
    Affiliation: Genome Centre, icddr,b
    Roles: writing - original draft; conceptualization; coding

  • Naimul Islam Faysal
    Affiliation: Genome Centre, icddr,b
    Roles: writing - original draft; conceptualization; coding

  • Tazkia Ahmed
    Affiliation: Genome Centre, icddr,b
    Roles: writing - original draft; conceptualization; coding

  • Tanzim Rahman
    Affiliation: Environmental Health and WASH, icddr,b
    Roles: writing - original draft; conceptualization; coding

Citation

You can cite these materials as:

Khan et al. 2025. “Introduction to Bacterial Genomics”, https://tahsinkhann.github.io/bacterial-genomics/1

Or, in BibTeX format:

@misc{khan2025-bactgen-site,
  title   = {Introduction to Bacterial Genomics},
  author  = {Khan, Tahsin and Rahman, Tanzim and Faysal, Naimul Islam and Ahmed, Tazkia},
  year    = {2025},
  url     = {https://tahsinkhann.github.io/bacterial-genomics/},
  urldate = {2025-09-16},
  note    = {Course website}
}
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Acknowledgements

This course has been designed following the training materials published by the University of Cambridge Bioinformatics Facility2‘3’4 and other open access training materials.

References

1.
Khan, T., Rahman, T., Faysal, N. I. & Ahmed, T. Introduction to bacterial genomics. (2025).
2.
Salehe, B. et al. Bioinfomartics for AWD-related pathogens. (2023).
3.
Asare, P. & Tonder, A. van. Introduction to bacterial genomics. (2023).
4.
Tonder, A. van, Tavares, H. & Salehe, B. Working with bacterial genomes. (2024).