CarveMe

CarveMe is a Python-based tool for the automated generation of genome-scale metabolic models from bacterial genomes. Given a FASTA file or DNA sequence as input, it predicts the uptake and secretion capabilities of an organism from genetic evidence alone, producing simulation-ready models without requiring manual gap-filling for any media. CarveMe is an official service of ELIXIR Norway and supports applications in biotechnology, microbiology, and systems biology.

Key Features

• Automated model reconstruction — builds genome-scale metabolic models directly from FASTA files via command-line invocations.
• Simulation-ready output — produces standardised models that can be used for simulation without manual gap-filling steps.
• Community modelling — supports generation of multi-species microbial community models from individual single-species models.
• Broad applicability — applicable across biotechnology, microbiology, and systems biology research contexts.
• Python-based — integrates into existing bioinformatics pipelines and scripting workflows.

Getting Started

1. Install CarveMe using pip.
2. Provide a genome in FASTA format as input.
3. Run the tool via the command line to generate a metabolic model.

Detailed documentation and source code are available on the CarveMe bio.tools page. The tool is distributed as a Python package, making it straightforward to incorporate into existing computational biology workflows.