SPECIMEN

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 ideas are welcome. Also, since its developemental, please note that bugs and error will probably occur. Please feel free to report them to the developers.

Currently avaible workflow:

• CMPB - CarveMe-ModelPolisher based:\Starting from a CarveMe draft model, refine and extend it towards a high-quality stain-specific model

• 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).

Note: Due to some major refactoring changes in refineGEMs this workflow might not run as expected.

• PGAB: under construction

Installation

Download this repository and run the command pip install -e . inside the top-level directory.

When running certain steps, further tools need to be installed:

• DIAMOND, version 2.0.4 or higher, needed for GeneGapFiller and HQTB
• EntrezDirect, if no NCBI mapping has been created beforehand

Quickstart

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.

Documentation

For more information about the available pipelines, the code or for troubleshooting, please refer to the documentation of the tool here.