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Data analysis of the south Wales Geochemical Gradient (SGG) 16S rRNA gene dataset

This repository contains all R and bash scripts utilised to process and analyse the SGG 16S rRNA gene dataset. Resulting data is under preparation for submission under the title "Hydrogeological controls of biogeochemically relevant bacterial consortia in subsurface mine waters", aimed at ISMEJ.

Folder organization and content:

  • 00_Data:

    SGG_hydro_and_geochemistry_v3_tidy_mM_wctls.csv contains all metadata used in this study.

    README_16S_download.txt contains links to download 16S rRNA gene FASTQ libraries.

  • 01_QC_Filtering:

    trim_16S_reads.sh trims and filters Illumina adapter sequences with cutadapt

  • 02_SV_Processing:

    DADA2_SGG_BDataPip.R uses DADA2 to infer SVs (sequence variants) from trimmed, quality-filtered FASTQs.

  • 03_Reports:

    SGG-Manuscript-Figures_Data_Pond.Rmd

    SGG-Manuscript-Figures_Data_Pond_BW.Rmd

    sgg_geochem.Rmd