Introduction to Metabarcoding and Metagenomics Analysis

16-19 April 2024




10 am - 3:30 pm




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:

£380/£400/£418 (University of Edinburgh/Other Universities/Industry)


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.



  • Urmi Trivedi, Head of Bioinformatics, Edinburgh Genomics  

  • Heleen De Weerd, Bioinformatician, Edinburgh Genomics

  • Nathan Medd, Training and Outreach Manager, Edinburgh Genomics 

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.


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



In this course we will cover the following topics:


  • Preprocess metabarcoding data using cutadapt

  • "Import" data into QIIME2

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

  • 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

  • Taxonomic classification of 16S long reads using NanoClust


Shotgun Metagenomics:

  • Data QC and Preprocessing of short reads

  • Taxonomic profiling using MetaPhlAn3

  • Functional profiling using HUMAnN3

  • Metagenome assembly using short reads using megahit

  • Contigs binning and generation of metagenome assembled genomes (MAGs)

  • Quality assessment of MAGs using CheckM

  • De-replication of MAGs

  • Taxonomic classification with GTDB-Tk

  • AMR analysis using AMR++

  • Data QC and Preprocessing of long reads

  • Taxonomic and Functional profiling using DIAMOND-MEGAN-LR

  • Metagenome assembly using long reads (Oxford Nanopore) using metaFlye

  • Assess the quality of assemblies using meta-QUAST and IDEEL

  • Generation of MAGs and assessment using SemiBin2