This repo contains a functional pipeline for analysing microbial communities in Mars analogs. Currently, it supports the data from Amils et al. 2023 for Río Tinto, an extreme environment on Spain.
This is the flowchart followed for the pipeline:
Information of the pipeline steps can be found in the notebooks folder:
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Preprocessing of supplementary data from Amils et al. 2023: 00-Data.ipynb
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Creation of genome-scale metabolic models (GEMs) using ModelSEEDpy: 01-GEM.ipynb
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Assessment of metabolic capabilities using RetroPath2.0: 02-RetroPath.ipynb
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Community analysis using MICOM: 03-MICOM.ipynb
Please, refer to the installation manual.
The pipeline uses many data sources with their respective licenses. A detailed guide on how to download and organise them is provided in the data readme.