MetaCoOc pre-formatted input files

Pre-formatted files for use in MetaCoOc.

Key components of MetaCoOc are:

Community profiles (presence/absence or abundance) derived from Metagenomes (e.g. those generated by singleM and hosted in Sandpiper)

Metadata about the metagenome samples e.g. the metadata submitted in NCBI SRA metagenome submissions

Parsing NCBI SRA Metadata

We adapted the parsing workflow was adapted from public_sequencing_metadata_corrections. The process is detailed in the README.md of metacooc

Formatting Sandpiper Data

We downloaded the community profiles in Sandpiper from Zenodo

The community profiles were formatted into Ingredients classes using MetaCoOc. The pickles of these are saved here.