Metagenomics Toolkit (MG-tk)
The Metagenomics Toolkit (MGtk) is a scalable, data-agnostic workflow for the automated analysis of metagenomic datasets derived from both short (Illumina) and long (Oxford Nanopore Technologies) reads. Designed for versatility, reproducibility, and minimal hardware requirements, MGtk streamlines the complete metagenomic analysis pipeline – from raw reads to annotated, interpretable genomes.
Key Benefits
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End-to-end automation: Covers all core steps of metagenome processing, from quality control to annotation.
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Cross-platform support: Compatible with Illumina and Oxford Nanopore datasets.
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Resource-efficient assembly: Integrates a machine-learning–optimized assembler that adjusts RAM requests dynamically to match actual needs, reducing dependence on high-memory servers.
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Comprehensive feature set: Beyond classical analysis, MGtk identifies plasmids, recovers unassembled taxa, and models microbial interdependencies.
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Modular and reproducible: Fully containerized for scalable use on local systems, HPC clusters, or the cloud.
Tools & Modules
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Quality Control & Preprocessing – Adapter trimming, quality filtering, and contamination screening.
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Assembly & Binning – Optimized short- and long-read assemblers with automatic parameter tuning.
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Annotation – Taxonomic and functional genome annotation with standardized outputs.
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Plasmid Identification – Integrates multiple tools for reliable plasmid detection and classification.
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Community Reconstruction – Recovery of unassembled members and dereplication for non-redundant genome sets.
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Microbial Interaction Modeling – Combines co-occurrence analysis with genome-scale metabolic models to explore ecological dependencies.
Applications
- Reconstruction of microbial community structure and function from complex metagenomes.
- Discovery of novel plasmids, symbionts, and microbial interactions in environmental or host-associated samples.
- Benchmarking and teaching of scalable metagenomics workflows.
- Predictive modeling of community metabolism and interspecies relationships.
Intended Use
The Metagenomics Toolkit is ideal for microbiome researchers, bioinformaticians, and systems biologists seeking a reproducible, resource-efficient workflow for analyzing metagenomic datasets from any sequencing platform.
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Service provision and maintenance funded by de.NBI.