Workshops and courses

Learning Pathway Building and Annotating Metagenome-Assembled Genomes (MAGs) from Metagenomics Reads

View event

Date: No date given

Language of instruction: English

This learning path will guide you through the process of constructing and analyzing Metagenome-Assembled Genomes (MAGs) using the Galaxy platform. You will explore the key steps involved in transforming raw metagenomic data into high-quality MAGs, from preprocessing to functional annotation.

By the end of this path, you will be able to:
- List and describe the essential steps in MAGs construction, including quality control, assembly, binning, and refinement.
- Define core concepts such as MAGs, binning, and functional annotation, and understand their significance in metagenomic analysis.
- Explain the importance of preprocessing metagenomic reads, focusing on quality control and contamination removal.
- Compare the quality of MAGs using metrics like completeness and contamination, and assess their suitability for downstream analysis.
- Evaluate the reliability of taxonomic assignments and functional annotations by leveraging reference databases.
- Analyze the relative abundance of microbial taxa in samples and infer ecological dynamics.
- Identify genomic features annotated by tools like Bakta, including coding sequences (CDS), rRNA, and tRNA.
- Interpret functional annotation results to uncover metabolic pathways, virulence factors, and other biological roles within microbial communities.

This path is designed to equip you with both the theoretical knowledge and practical skills needed to confidently construct, evaluate, and analyze MAGs in your research.

Keywords: microbiome

Learning objectives:

  • Analyze the relative abundance of microbial taxa in the samples and infer ecological dynamics.
  • Assess long reads FASTQ quality using Nanoplot and PycoQC
  • Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
  • Assess the quality of MAGs and determine whether they meet standards for downstream analysis.
  • Compare the quality of MAGs based on completeness, contamination, and other metrics.
  • Construct and apply simple assembly pipelines on short read data.
  • Define essential terms such as MAGs (Metagenome-Assembled Genomes), binning, and functional annotation.
  • Describe common challenges in metagenomics binning.
  • Describe the purpose and process of assembling, binning, and refining MAGs.
  • Describe what an assembly is.
  • Describe what is metagenomics binning.
  • Evaluate the annotation
  • Evaluate the quality of the Assembly with QUAST, Bowtie2, and CoverM-Contig.
  • Evaluate the reliability of taxonomic assignments and functional annotations based on reference databases.
  • Evaluation of MAG quality and completeness using CheckM software.
  • Explain how tools based on de Bruijn graph work.
  • Explain the difference between co-assembly and individual assembly.
  • Explain the difference between reads, contigs and scaffolds.
  • Explain the importance of preprocessing metagenomic reads, including quality control and contamination removal.
  • Familiarize yourself with the basics of Galaxy
  • Get information about ARGs
  • Identify reads originating from contaminants or host genomes.
  • Identify the types of genomic features annotated by Bakta (e.g., CDS, rRNA, tRNA).
  • Interpret the functional annotation results to identify metabolic pathways, virulence factors, and other biological roles.
  • Learn how histories work
  • Learn how to create a workflow
  • Learn how to extract and run a workflow
  • Learn how to obtain data from external sources
  • Learn how to run tools
  • Learn how to share a history
  • Learn how to share your work
  • Learn how to upload a file
  • Learn how to use a tool
  • Learn how to view histories
  • Learn how to view results
  • List the key steps involved in MAGs building from raw data.
  • Perform metagenomic binning using MetaBAT 2 software.
  • Perform quality correction with Cutadapt (short reads)
  • Process single-end and paired-end data
  • Process the outputs to formate them for visualization needs
  • Remove those reads to produce high-quality, clean metagenomic data suitable for downstream analyses.
  • Run a series of tool to annotate a draft bacterial genome for different types of genomic components
  • Run a series of tool to assess the presence of antimicrobial resistance genes (ARG)
  • Summarise quality metrics MultiQC
  • Summarize how taxonomic assignment and functional annotation contribute to understanding microbial communities.
  • Visualize a draft bacterial genome and its annotations
  • Visualize the ARGs and plasmid genes in their genomic context

Event types:

  • Workshops and courses

Sponsors: ABRomics, Australian BioCommons, Avans Hogeschool, ELIXIR Europe, Erasmus Medical Center, Institut Français de Bioinformatique, Melbourne Bioinformatics, The Pennsylvania State University, The University of Melbourne, University of Freiburg, de.NBI

Scientific topics: Metagenomics, Sequence assembly, Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements, Public health and epidemiology, Infectious disease, Antimicrobial resistance

Activity log