panDraft is a tool for reconstructing species-level genome-scale metabolic models (GEMs) by combining the strengths of multiple draft models derived from MAGs (Metagenome-Assembled Genomes). When your MAGs are a little too incomplete or a bit messy, panDraft steps in to fill the gaps—literally.
Instead of relying on a single MAG, panDraft integrates multiple related models and performs a pan-reactome analysis to capture the full metabolic potential of a species. This means you can build a more complete and representative GEM for your taxa of interest.
MAGs are often fragmented and missing key functions. As a concequence draft-GEMs built from MAGs are usually incomplete. panDraft helps you recover lost metabolic pathways by pooling information across related genomes. Think of it as creating a metabolic "supermodel" for your species, built from its best parts!
panDraft is an extension of the gapseq framework. It uses:
- Draft models (.RDS) from individual MAGs
- Reaction weight files (*-rxnWeights.RDS)
- Gene-to-reaction association files (*-rxnXgenes.RDS)
- Pathway summaries (*-all-Pathways.tbl)
These are merged to produce a pan-species GEM that better represents the functional potential of the taxa.
Since panDraft is part of the gapseq toolkit, please refer to the official gapseq GitHub page for:
- Installation instructions
- Example workflows
- Detailed documentation
- License information
Feedback, ideas, and contributions are welcome—feel free to open an issue or a pull request!
De Bernardini, N., Zampieri, G., Campanaro, S., Zimmermann, J., Waschina, S. & Treu, L. pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes. Genome Biol 25, 280 (2024). https://doi.org/10.1186/s13059-024-03425-1