3 min read

Module 15: Taxonomic analysis

2024-01-27

Overview

Module 15 is centered on taxonomic analysis, a fundamental aspect of microbial genomics that involves classifying organisms into their respective taxa based on genetic information. This module will introduce students to the principles of taxonomic classification and the use of computational tools, such as Kraken2, for rapid and accurate taxonomic assignment of sequencing data. Students will learn about the methodologies for analyzing metagenomic datasets, the challenges of taxonomic resolution at different levels, and the importance of taxonomic analysis in understanding microbial diversity, ecology, and evolution. Practical labs will provide hands-on experience with Kraken2, enabling students to conduct taxonomic analysis on real-world datasets.

Introduction

  • The role of taxonomic analysis in microbial genomics and its applications in research, clinical diagnostics, and environmental studies
  • An overview of the taxonomic hierarchy and the criteria used for classifying organisms
  • The challenges of taxonomic classification in the era of high-throughput sequencing

Topics

Principles of Taxonomic Analysis

  • Understanding the taxonomic framework and the use of genetic markers for classification
  • The importance of reference databases in taxonomic assignment
  • The concept of taxonomic resolution and its implications for analysis

Kraken2 for Taxonomic Analysis

  • Introduction to Kraken2 and its algorithm for taxonomic classification
  • The advantages of Kraken2 in terms of speed and accuracy
  • Preparing input data and reference databases for Kraken2 analysis

Running Taxonomic Analysis with Kraken2

  • Detailed walkthrough of the Kraken2 workflow, from database construction to classification
  • Interpreting the output of Kraken2 and understanding the confidence scores
  • Best practices for validating and refining taxonomic assignments

Applications of Taxonomic Analysis

  • The use of taxonomic analysis in metagenomics to study microbial communities
  • Taxonomic profiling in clinical microbiology for pathogen identification
  • Environmental monitoring and biodiversity assessment through taxonomic analysis

Challenges in Taxonomic Analysis

  • Dealing with the complexities of metagenomic data, such as mixed communities and novel organisms
  • Addressing the limitations of reference databases and the potential for misclassification
  • Strategies for improving taxonomic resolution and accuracy

Labs

  • Lab 1: Setting Up Kraken2 and Building Custom Databases
  • Lab 2: Taxonomic Classification of Metagenomic Sequencing Data with Kraken2
  • Lab 3: Interpreting and Validating Taxonomic Analysis Results

Learning Outcomes

By the end of this module, students will be able to:

  • Describe the principles of taxonomic analysis and its significance in the study of microbial genomics.
  • Use Kraken2 to perform rapid taxonomic classification of sequencing data.
  • Interpret the results of taxonomic analysis and assess the confidence of taxonomic assignments.
  • Apply taxonomic analysis to various fields, including environmental microbiology, clinical diagnostics, and biodiversity research.
  • Address the challenges associated with taxonomic classification in complex datasets.
  • Communicate the outcomes of taxonomic analysis effectively in scientific and non-scientific contexts.