Introduction to Metagenomic Data Analysis

Coming Soon

The Material from this course is included in our combinded Metagenomic and Metabarcoding course coming up in October 2022



TBC 2022, 10.00 - 15:00 




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:



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.

"Great course, lots learnt behind the theory and practice" (September 2021)

"Thanks Urmi for the in-depth metagenomics course really enjoyed it!!" (September 2021)


  • 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.


  • 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:

  • 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
  • Data QC and Preprocessing of long reads
  • Metagenome assembly using long reads (Oxford Nanopore) using metaFlye
  • Polishing long read assembly with Marginpolish , HELEN and Racon
  • Assess the quality of assemblies using QUAST and IDEEL