Input files for the statistical analysis of bacterial and fungal metabarcoding data along an olive farm-to-food continuum (Horizon Europe DOMINO project)

This dataset contains the input files for the downstream statistical analyses and figures of the manuscript "Microbial continuity across an olive farm-to-food continuum reveals stable reservoirs, ecological filtering and microbiome transmission" (submitted to Environmental Microbiome). 

Raw reads: ENA under accession PRJEB108463. ASV tables were generated with MetaFlux (https://github.com/iLivius/MetaFlux).

Link to the GitHub repository: https://github.com/chiaratraina-eng/statistics-environmental-microbiome-CT.

Files (in DOMINO_merged.zip):

• bac_meta_full.tsv: sample metadata (one row per sample; columns = Sample, Area, Tree, Compartment, Replicate, Time, Year);
• bac/ and fun/03.dada2_output/asv_table.txt: ASV tables (rows = ASVs; columns = samples; last column = taxonomy);
• bac/ and fun/04.stats/02.filtered_reads.txt: read counts per sample at each processing step (one row per sample; columns = raw, filtered, denoised, merged, non-chimeric).

Abbreviations: CNEG = negative controls; CPOS = positive controls.