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Module 3: Basics of bacteria WGS analyses

2024-01-27

Overview:

This module is designed to provide you with a comprehensive understanding of the Whole Genome Sequencing (WGS) process, from the initial sequencing data to the assembly and mapping of bacterial genomes. By the end of this module, students will be familiar with the common file formats used in WGS, the principles of de novo assembly, and the basics of read mapping. This knowledge is crucial for anyone looking to work in the field of bacterial genomics, as it forms the basis for more advanced analyses such as variant calling, phylogenetics, and comparative genomics.

Topics:

Introduction:

  • Overview of Whole Genome Sequencing (WGS) and its importance in bacterial genomics.
  • The workflow of WGS, including sample preparation, sequencing, data processing, and analysis.
  • Challenges and considerations specific to bacterial WGS, such as the presence of plasmids, horizontal gene transfer, and repetitive elements.

File Formats:

  • Introduction to the most common file formats encountered in WGS, including FASTQ, FASTA, SAM/BAM, and VCF.
  • Understanding the structure and content of these file formats and their role in the WGS pipeline.
  • Best practices for handling and converting between different file formats.

Introduction to De Novo Assembly:

  • The concept of de novo assembly and its significance in reconstructing bacterial genomes without a reference.
  • Overview of assembly algorithms and software commonly used for bacterial genomes, such as SPAdes, Velvet, and Canu.
  • Evaluation of assembly quality and how to interpret metrics like N50, coverage, and contig length.

Reads Mapping:

  • The principles of read mapping and its role in comparing sequencing reads to a reference genome.
  • Introduction to alignment algorithms and tools such as BWA, Bowtie2, and SAMtools.
  • Understanding the output of read mapping and how to utilize it for downstream analyses.

Learning Outcomes:

Upon completion of this module, students will be able to:

  • Recognize and work with various file formats used in bacterial WGS.
  • Understand the principles and steps involved in de novo genome assembly.
  • Understand when and how to choose between de novo assembly and read mapping in downstream analyses