Learning Pathway Building and Annotating Metagenome-Assembled Genomes (MAGs) from Metagenomics Reads
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:
- Assess long reads FASTQ quality using Nanoplot and PycoQC
- Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
- Construct and apply simple assembly pipelines on short read data.
- Describe common challenges in metagenomics binning.
- 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.
- 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.
- Familiarize yourself with the basics of Galaxy
- Get information about ARGs
- 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
- 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
- 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
- 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, The Pennsylvania State University, 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
