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Module 9: Gene set completeness analysis

2024-01-27

Overview

Module 9 delves into the critical evaluation of gene set completeness in bacterial genomics. This process is essential for assessing the quality and integrity of genome assemblies and annotations. The module will explore the concept of gene set completeness, the tools and methods used to assess it, such as the use of single-copy orthologs and benchmarking universal single-copy genes (BUSCO), and the implications of completeness in downstream genomic analyses. Through practical labs, students will learn how to perform gene set completeness analysis and interpret the results to ensure robust genomic studies.

Introduction

  • Understanding gene set completeness and its importance in genome assembly and annotation
  • The impact of gene set completeness on comparative genomics and evolutionary studies
  • Overview of the tools and metrics used to assess gene set completeness

Topics

Fundamentals of Gene Set Completeness

  • Defining gene set completeness in the context of bacterial genomics
  • The relationship between completeness, contiguity, and quality of genome assemblies

Tools for Assessing Gene Set Completeness

  • Introduction to tools like BUSCO and CheckM
  • The use of core genes and single-copy orthologs as indicators of completeness

Methodologies for Completeness Analysis

  • Step-by-step guide to performing gene set completeness analysis
  • Understanding the output and metrics provided by completeness assessment tools

Addressing Incompleteness

  • Strategies for improving gene set completeness in genome assemblies
  • The role of sequencing depth, assembly algorithms, and manual curation

Implications of Gene Set Completeness

  • The consequences of incomplete gene sets on functional annotation and downstream analyses
  • Case studies highlighting the importance of completeness in bacterial genomics research

Labs

  • Lab 1: Assessing Gene Set Completeness with BUSCO
  • Lab 2: Using CheckM for Completeness and Contamination Analysis
  • Lab 3: Improving Gene Set Completeness through Assembly Refinement

Learning Outcomes

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

  • Define gene set completeness and explain its significance in the context of bacterial genome assembly and annotation.
  • Utilize computational tools to assess the completeness of gene sets in bacterial genomes.
  • Interpret the results of gene set completeness analysis and understand the implications for genomic research.
  • Implement strategies to address issues of incompleteness in genome assemblies.
  • Critically evaluate the quality of bacterial genome assemblies based on completeness metrics.
  • Communicate the findings of gene set completeness analyses effectively in both written and oral formats.