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A high-throughput genome-scale metabolic reconstruction and growth simulation pipeline.

Bactabolize is designed for rapid generation of strain-specific metabolic reconstructions from bacterial genome data using the approach described in Norsigian et al. Nature Protocols 2020. It leverages the COBRApy toolkit and takes an input genome assembly (annotated or unannotated) to construct a strain-specific draft model by comparison to a reference (ideally a multi-strain or 'pan'-reference model). It also allows high-throughput growth phenotype simulation via Flux Balance Analysis (FBA) e.g. to predict substrate usage profiles and Single Gene Knockout analysis (SGK) to predict the impacts of single gene knockout mutations. These can be performed under a variety of growth conditions and mediums.

Bactabolize was developed by Stephen Watts, Ben Vezina and Kelly Wyres and is available for use, reuse and adaptation under a public GNU v3 license. We thank Jane Hawkey, Helena Cooper, Kathryn Holt, Jon Monk and Sylvain Brisse for their important contributions.

If you use Bactabolize in your research please cite Vezina / Watts et al. Bactabolize. In prep.

Use the navigation menu on the right to find out more about Bactabolize and how to use it.