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Course Description

Metagenomics, the sequencing of DNA directly from a sample without first culturing and isolating the organisms, has become the principal tool of “meta-omic” analysis. It can be used to explore the diversity, function, and ecology of microbial communities. The CBW has developed a 3-day course providing an introduction to metagenomic data analysis followed by hands-on practical tutorials demonstrating the use of metagenome analysis tools. The tutorials are designed as self-contained units that include example data and detailed instructions for installation of all required bioinformatics tools.

Participants will gain practical experience and skills to be able to:

  • Design appropriate microbiome-focused experiments
  • Understand the advantages and limitations of metagenomic data analysis
  • Devise an appropriate bioinformatics workflow for processing and analyzing metagenomic sequence data (marker-gene, shotgun metagenomic, and metatranscriptomic data)
  • Apply appropriate statistics to undertake rigorous data analysis
  • Visualize datasets to gain intuitive insights into the composition and/or activity of their data set

Target Audience

Graduates, postgraduates, staff bioinformaticians and PIs working with or about to embark on analysis of marker genes, metagenomic, and metatranscriptomic data from microbiome-focused experiments.

Course Outline

Module 1: Introduction to Metagenomics

  • A brief history of microbiome studies
  • Review of relevant terms (microbial communities, microbiome, species, metagenome, marker genes, metatranscriptomics)
  • Technologies used in meta’omics

Module 2: Taxonomic Analysis + Stats Module

  • What is 16S? Why is it useful? What are its limitations? Methods
  • 16S data processing
  • Clustering and Classification – OTUs vs. ASVs ; Taxonomy
  • Diversity (and co-occurrence?)
  • Statistics and machine learning related to microbiome studies

Lab Practical

Module 3: Bridging Taxonomy and Function

  • Brief intro on gene annotations and different granularity
  • Inferring function from taxa
  • Different methods for functional prediction
  • Focus on PICRUSt2
  • Limitations of all prediction methods

Lab Practical

Module 4: Metagenomics Functional

  • Non-assembly (this section) versus assembly based approache
  • Filtering out host reads (especially in low microbial load samples)
  • Metagenomics taxa using Kraken & Braken
  • Metagenomics function using HUMAnN or DIY (mmseqs)
  • Correction for read length, genome size, etc. (microbecensus)
  • Stratified functional tables (e.g. linking functions from the taxa they originate from)
  • Driver versus passenger functional selections
  • Special functions (e.g. AMR genes)

Lab Practical

Module 5: Metagenome Assembly, Binning, and Extracting Genomes from Metagenomes

  • Overview of binning theory/approaches, advantages/disadvantages
  • Insights from prior studies
  • Overview of suggested workflow

Lab Practical

Module 6: Metatranscriptomics

  • What is metatranscriptomics (Metatranscriptomics v RNASeq)
  • Why metatranscriptomics
  • Sample collection and library generation
  • Processing pipelines, filtering, functional and taxonomic annotation
  • Read normalization and differential gene expression
  • Pathway enrichment
  • Visualization

Lab Practical

Module 7: Sampling and Sample Processing considerations

  • Experimental design and sample preparation considerations

Module 8: Biomarkers Keynote Lecture

  • Benefits and applications of biomarkers
  • Types of markers – taxonomic, functional
  • Examples of existing biomarkers
  • Methods for identifying new markers
  • Normalization, copy number variation, and other considerations
  • Finding differential features: categorical, correlative
  • Ranking features
  • Network-based analysis
  • Towards a genetic test: Designing PCR/qPCR primers/tests
  • Example of biomarker ID success
  • General considerations, cautionary notes

Workshop Details:

Duration: 3 days

Start: Sep 01, 2021

End: Sep 03, 2021

Location:

Course Mode: Online

Status: Registration Closed

Workshop Started

Offers:

CAD $389 for applications received between March 18, 2021 to June 30, 2021
CAD $524 for applications received between July 1, 2021 to August 23, 2021
Limited to: 40 participants

Open Access Content:

Canadian Bioinformatics Workshops promotes open access. Past workshop content is available under a Creative Commons License.

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