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README.md

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Intro

This repository contains data obtained from preprocessing raw fastq files into ASV and taxonomic tables.


Structure of the repository

  • aggregated-tables: data directory containing count tables aggregated at all taxonomic levels (Phylum, Class, Order, etc.) for each study;
  • analysis-combined: data directory containing (1) plots generated by the scripts in scripts/analysis-combined/, which were used to make the paper figures, and (2) .rds or .csv files saved as checkpoints;
  • analysis-individual: data directory containing all outputs generated by the scripts in scripts/analysis-individual/, including but not limited to, .fastq files of quality-filtered reads, .rds files saved as checkpoints, and folders for running some steps on a high-computing cluster;
  • asv-sequences: data directory containing all ASV sequences imputed from the DADA2 algorithm for each dataset;
  • phyloseq-objects: data directory containing the phyloseq objects for each dataset, ready for analysis!

More details on how this data was obtained are provided in REAME.md files within each directory (hint: scripts to generate this data are in the scripts/ directory).