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Bioinformatics
magprofile
Reproducible pipeline for genome-resolved microbiome ecology from assembly to network inference.
Problem
The analytical path from metagenome-assembled genomes (MAGs) to ecologically interpretable outputs is fragmented across ad hoc scripts that undermine reproducibility and mishandle compositional data.
Methods
Python
R
Snakemake
SqueezeMeta
Docker/Singularity
Role
Sole Developer
Key Outcomes
- Unified five analytical stages into a single YAML-configurable pipeline
- Processed 1,022 MAGs across 30 metagenome samples in ~105 minutes
- Generated 30 publication-ready figures with compositionally-aware statistics
Metrics
1,022 MAGs processed
633 MAGs passed quality filtering
9,166 network edges inferred
30 publication-ready figures generated