What You Will Learn
Day 1: Basics
- Linux Basics: A short step-by-step guide to navigating the command-line interface, ensuring all participants are ready for the computational aspects of the workshop.
- Introduction to Metagenomics: Overview of metagenomics workflows, including pre-processing, quality checks, and error handling for sequencing data.
- Basics of Nextflow: Learn the fundamentals of Nextflow scripting to create scalable and reproducible bioinformatics workflows.
Day 2: Metagenomic Workflows
- nf-core Pipelines: An introduction to the nf-core community and how its workflows can simplify metagenomic data analysis.
- Taxonomy Profiling: Explore methods and tools for identifying and classifying microbial species in sequencing datasets.
- Hands-On Practical: Taxonomy Profiling with Nextflow: Apply what you’ve learned in a guided session on running taxonomy profiling workflows using nf-core.
- Assembly and Binning: Learn how to reconstruct genomes from metagenomic data using assembly and binning techniques.
- Classification and Annotation: Discover methods to classify and annotate metagenomic reads, contigs, and bins for functional analysis.
- Practical Session: MG-tk and MAG Pipelines: Work on real data using MG-tk and MAG tools, focusing on best practices for metagenome data pre-processing, assembly, and binning.
Day 3: Workflow Automation and Closing Remarks
- Cloud Workflow Management (CLOWM): Introduction to managing metagenomic workflows in a cloud environment, enabling efficient data processing.
- Running Workflows in CLOWM: Hands-on practice executing workflows on the de.NBI cloud.
- Open Discussion: Wrap up the course with a Q&A and feedback session to address specific challenges and share ideas for future directions.
