Introduction
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, CarveMe predicts the uptake and secretion capabilities of an organism from genetic evidence alone and produces simulation-ready models without gap-filling for any media. It also supports the generation of microbial community models from single-species models. CarveMe is an official service of ELIXIR Norway.
Key Features
- Automated model reconstruction — build genome-scale metabolic models directly from FASTA files via simple command-line invocations
- Simulation-ready output — produces standardised models that can run without manual gap-filling
- Community modelling — generate multi-species community models from individual organism models
- Broad applicability — supports diverse applications in biotechnology, microbiology, and systems biology
- Python-based — integrates easily into existing bioinformatics pipelines and scripting workflows
Getting Started
Install CarveMe via pip and provide a genome (FASTA format) to generate your first metabolic model. Detailed documentation and source code are available on the CarveMe bio.tools page.