SPECIMEN is a collection of different workflows designed for the automated and standardised curation of genome-scale models. It is mainly based on the refineGEMs toolbox, but also includes additional tools like CarveMe.
Note: This tool is currently still under active developement, any feedback or ides are welcome.
Currently avaible workflow:
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CMPB - CarveMe-ModelPolisher based:\Starting from a CarveMe draft model, refine and extend it towards a high-quality stain-specific model
Note: For a future update, optional direct integration of CarveMe into the pipeline is planned
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HQTB - High-quality template based:\This pipeline follows the modelling approach of using a high-quality template model as a basis for the reconstruction of a new model from a new genome (e.g. a different strain).
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PGAB: under construction
Download this repository and run the command pip install -e . inside the top-level directory.
When running the HQTB Pipeline, further tools need to be installed:
- DIAMOND, version 2.0.4 or higher
- EntrezDirect, if no NCBI mapping has been created beforehand
After the installation, main functionalities can be accessed either via the command line. Try running specimen --help for more information.
For greater control or for further integration into other scripts, the modules of SPECIMEN can be loaded as a Python package using import specimen in a Python script.
For more information about the available pipelines, the code or for troubleshooting, please refer to the documentation of the tool here.