Introduction to metagenomics

Last updated on 2026-04-28 | Edit this page

Estimated time: 20 minutes

Overview

Questions

  • What is metagenomics?
  • What are the applications of metagenomics?
  • What are the advantages of using metagenomics?
  • What is the difference between metagenomic profiling and genome-resolved metagenomics (MAGs)

Objectives

  • Define metagenomics.
  • Explain the difference between metagenomics and amplicon sequencing.
  • Describe main approaches for metagenomic profiling.
  • Explain what a “metagenome-assembled genome” (MAG) is.
  • Bonus: be able to explain that to a layperson at a party!
Key Points
  • Metagenomics sequences all DNA, giving an unbiased, high-resolution view of community composition and function—beyond what amplicon sequencing can capture.
  • Reads profiling delivers fast, reference-based taxonomic and functional counts data for downstream analyses like TaxSEA and integration workflows.
  • MAGs can be reconstructed via assembly and binning of reads, revealing uncultured lineages and their metabolic potential.
  • Modern sequencing and workflows (short-reads, long-reads, hybrids; nf-core pipelines) improve accuracy, assembly quality, and reproducibility.