Code used for this paper:
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display_items/ - Raw image files generated by plotting scripts.
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scripts/
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dataset_running/ - Code for running POMS on Almeida and TARA oceans datasets.
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display_items/ - Code for generating all figures.
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general_processing/ - General Python scripts used for processing raw datasets
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preprocessing/ - Code used for preprocessing specific datasets to be in format used downstream.
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simulations/ - Code used to run metagenome-assembled genome (MAG.based; described in main text) and the simulations based on reference genomes only (ref.based; described in supplement).
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text_stats/ - Code to parse key statistics to report in main text.
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POMS_manuscript_functions.R - Functions used for multiple scripts.
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alt_tool_functions.R - Functions used for running standard differential abundance tools.
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Note that the key datafiles for this project are available on FigShare.