Home - egenomics/agb2025 GitHub Wiki
Welcome to the AGB 2025 Wiki!
This wiki serves as the central hub for documentation, guidelines, and collaborative development within the HdMBioinfo Group. The project aims to establish a standardized and clinically relevant workflow for microbiome data processing, supporting applications in precision medicine, diagnostics, and microbiome research.
What You’ll Find Here:
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General Overview
Context, clinical rationale and high level objectives. -
Data Management Plan
Storage, retention, access control and security policies. -
File Nomenclature Key concepts, naming conventions and the official metadata dictionary.
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Modules Modular workflow diagrams, tool selection, QC checkpoints and container profiles.
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Result Integration and Clinical Reporting Data Upload, Taxonomy, Diversity, Lifestyle, Report Summary
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Validation
Tip: Use the sidebar or the table of contents at the top of each page to navigate quickly.
Purpose
This wiki exists to:
- Reduce onboarding time for new team-mates and external collaborators.
- Document decisions - why we chose a tool, a threshold, a naming scheme.
- Serve as living documentation of the wiki itself, outlining its structure, update rules and style guide.
- Keep everyone aligned across wet lab, bioinformatics and clinical teams.
General overview
Data Management Plan (DMP)
Directory Structure
File Nomenclature
Metadata
Nextflow Pipeline
Data Preprocessing and Quality Control
Taxonomic and Functional Analysis
Result Integration and Clinical Reporting
Validation
Pages of the group:
Group 1 Group 2 A Group 2 B Group 3 Group 4