Metagenomics and Metabarcoding




Wednesday 28 - Friday 30 August, 09:00 - 17:00 


Peter Wilson Building (Room G155), The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK


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:


You can cancel up to one month before the workshop and receive a refund minus 30% for administration.


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 shotgun metagenomics and 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.

You will then be introduced to methods used for assembly from metagenomics samples. Attendees will use tools to assemble metagenome assembled genomes (MAGs) from short read and long read data. We will discuss the different approaches and tools available for these assemblies and the benefits and limitations of each options.



  • Urmi Trivedi, Bioinformatician, Edinburgh Genomics  

  • Amanda Warr, Research Geneticist, Roslin Institute 

  • Rob Stewart , Bioinformatician, Roslin Institute

  • Albert Phillimore, Institute of Evolutionary Biology, University of Edinburgh (guest lecturer)

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

Workshop format

The 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.


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



By the end of the course students should be familiar with:

  • Tools available to assemble MAGs from short and long read data.

  • Extraction taxonomic and functional features from shotgun metagenomic data

  • Generation ASV/OTU tables, taxonomy assignment and performing diversity analysis

  • Quality control of the metagenomic data