Introduction to Metabarcoding

 

Date:

TBD, 9:30 - 15:00 

Venue:

Online

Places:

25 for each workshop

You will be contacted by our finance team for full payment. Once payment is made, your place will be confirmed and full details sent by our training team.

Registration fee:

£TBD

Information:

Contact our training team

 

The ability to identify organisms from traces of genetic material in environmental samples has reshaped the way we see life on earth. Especially for microorganisms, where traditional identification is hard or near impossible, metagenomic techniques have granted us unprecedented insight into the microbiome of animals and the environment more broadly.

This course focuses on the computational methods used to analyse the wealth of data produced by metabarcoding (Amplicon targeted metagenomics) studies.

This course will provide you the insights to the DNA metabarcoding analyses from preprocessing and quality control of the raw data to the construction of OTU/ASV tables, taxon assignment, diversity analysis and differential abundance analysis using QIIME2. Further, you will also learn about methods to generate the reference-based profile to generate microbial community features like taxonomic abundances or functional profile and how to identify the ones characterizing differences between two biological conditions.

 

Instructors

  • Urmi Trivedi, Bioinformatician, Edinburgh Genomics  

  • Nathan Medd, Training and Outreach Manager, Edinburgh Genomics (demonstrator)

Workshop format

This live online workshop consists of presentations and hands-on tutorials.

Who should attend

Graduates, postgraduates, and PIs, who are using, or planning to use, metagenomic technology in their research and want to learn how to process and analyse the data produced.

Requirements

  • A general understanding of molecular biology and genomics.
  • A working knowledge of Linux at the level of the Edinburgh Genomics Linux for Genomics workshop.

 

Outcomes

By the end of the course students should be able to:

  • Preprocess metabarcoding data using cutadapt 

  • "Import" data into QIIME2 

  • Do quality filtering, denoising and picking of features and representative sequences (ASV) using DADA2 

  • Generate OTU sequences using VSEARCH from QIIME2 

  • Assign taxonomy to features with trained classifiers. 

  • Align sequences and build a phylogenetic tree. 

  • Calculate alpha and beta diversity 

  • Perform differential abundance analysis between groups using ANCOM