SC.SkagerrakMTB

This repository contains data and code associated with the publication:

"Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA"
Holman LE, Zampirolo G, Gyllencreutz R, Scourse J, Frøslev T, Carøe C, Gopalakrishnan S, Pedersen MW, Bohmann K (2025)
Published in Molecular Ecology Resources
📄 Read the paper

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Repository Structure

File/Folder	Description
0.1.Bioinformatics.R	R-based processing and formatting of metabarcoding eDNA data for downstream analysis
0.1.TaxonomicAssignment.sh	Shell script for assigning taxonomy to metabarcoding reads using reference databases
0.2.FilePrep..R	Formats and merges metabarcoding read tables for analysis
0.3_Giulia_Damage_profiles_MTG.R	Generates DNA damage profiles for metagenomic data
0.4.1_Validation_Outlier.sh	Shell script to detect and inspect outlier samples
0.4.2_SupplementaryMTG.R	R script to generate supplementary analyses for MTG datasets
1.Analysis.R	Main analysis script: diversity estimates, comparative analyses, and figure generation
filtered_metazoan_all.csv	Filtered metazoan taxa table (metagenomics)
filtered_genus_all.csv	Filtered genus-level taxa table (metagenomics)
MTB.metadata.csv	Metadata file for metabarcoding samples
MTB.reads.csv	Read count table for metabarcoding samples
MTG.metadataAge.csv	Metadata and age model data for metagenomics samples
MTG.reads.csv	Read count table (metagenomics, CSV version)
MTG.reads.xlsx	Read count table (metagenomics, Excel version)
rawData/	Raw or minimally processed input files (e.g. unfiltered outputs)
cleanedData/	Cleaned and filtered data used in analyses
figures/	Output figures included in the manuscript and supplementary materials
taxonomy/	Taxonomy files for metabarcoding
README.md	This file

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