Thesis Dataset Part 1 of 3

This archive contains the complete dataset backup and supporting materials used in:

Freiheit, M.N. (2025). Development of Reproducible Metagenomic Approaches for Skin and Wound Microbiome Analysis. University of Hull.

The archive provides a comprehensive collection of all non-workflow materials generated and used throughout the project, ensuring full transparency and reproducibility of the analyses presented in the thesis.

Contents include:

Raw sequencing data (where permissible)

Processed data files and intermediate outputs

Metadata files and sample information tables

Library tables and taxonomic result tables

Scripts used for downstream analyses and figure generation (R, Python, Bash)

Input files and scripts used to generate thesis figures

Supplementary analysis scripts not included in workflow pipelines

Adaptive sequencing resources, including:

Installation files and setup scripts

Reference files and configurations

Supporting scripts for ReadFish and adaptive sampling analyses

Miscellaneous project files required to reproduce results and figures

All materials are provided as used during the project, including original scripts and data structures, to preserve the full context of the analyses. While workflows standardise major processing steps, this archive captures additional exploratory analyses, figure generation workflows, and supporting data not encapsulated within the main pipelines.

This dataset is intended to enable:

Full reproduction of figures and results presented in the thesis

Verification of intermediate analysis steps

Exploration of alternative analytical approaches using the same data

The corresponding workflow repositories are available on GitHub:

MMCAW: https://github.com/merfre/MMCAW

ASAW: https://github.com/merfre/Adaptive_Sequencing_Analysis_Workflow

DBCW: https://github.com/merfre/Database_Creation_Workflow

This record serves as the index for the complete thesis dataset backup. Due to Zenodo record size limits, the full archive is distributed across three linked records:

Part 1 DOI: 10.5281/zenodo.17752007

Part 2 DOI: 10.5281/zenodo.19659286

Part 3 DOI: 10.5281/zenodo.19659303

To complete this dataset download the three parts listed above and run this code:cat thesis_dataset_* > thesis_dataset.tar.gz