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This repository contains additional matrials for the following preprint:

Micom: metagenome-scale modeling to infer metabolic interactions in the microbiota.
Christian Diener and Osbaldo Resendis-Antonio
https://doi.org/10.1101/361907

All scripts are provided as Python 3 code. libraries required to reproduce figures and data processing csan be installed using the provided requirements file:

pip install --user -r requirements.txt

See each subfolder for detailed desription of contained files.

figures
Scripts to reproduce the figures in the publication.

results
Intermediate results required for figures.

workflows
Long running parallel analyses that produce the results provided in the previous folder.

genera.py
Reads the genus-level abundances and combines them with the AGORA models for each genus.
Output: genera.csv

taxa_stats.py
Counts the fraction of reads assigned to each taxonomic rank and the fraction of reads that has at least one represenative in the AGORA models.
Output: a text table

recent.csv Provides a list of samples and the corresponding SRA abundances.