Datasets for "Reference library readiness for eDNA: A multi-marker gap analysis and prioritization roadmap of Philippine marine fishes"
Description
These datasets accompany the manuscript “Reference library readiness for eDNA: a multi-marker gap analysis and prioritization roadmap of Philippine marine fishes”. It contains the raw input files, repository data package, Python processing and retrieval scripts, intermediate harmonised tables, downstream R analysis scripts, and exported summary outputs required to reproduce and audit the taxonomic harmonisation, sequence-record retrieval, marker-coverage summaries, accession/record-depth analyses, family-level comparisons, provenance analyses, and manuscript figure generation presented in the study. The workflow begins with a curated species list used for WoRMS-based taxonomic harmonisation. That harmonisation step generates the standardised species backbone and related tracking files used to support downstream repository processing. The WoRMS-derived outputs, including the harmonised species table and repository retrieval name list, are then used as inputs for both the GenBank and BOLD workflows. The GenBank workflow uses the WoRMS-harmonised inputs to retrieve and screen repository records, producing a resolved record-level feature table and downstream summary products including per-species marker coverage, per-species accession depth, marker-depth summaries, marker-presence summaries, family-level coverage tables, marker-tier summaries, and diagnostic outputs. The BOLD workflow uses the same harmonised taxonomic inputs together with the archived public BOLD data package BOLD_Public.26-Sep-2025.tar.gz. This produces the initial BOLD record table and quality-control outputs. Because some target species were not represented in the public-package-derived record set, the workflow also incorporates a patching step based on a legacy minimal record file from a discontinued API retrieval workflow. The patched final record table is then used to generate resolved per-species marker coverage tables, per-species record-depth summaries, marker-depth summaries, marker-tier summaries, marker-presence summaries, family-level coverage tables, and diagnostic outputs. Downstream analyses are performed in R using the processed GenBank and BOLD outputs. These scripts generate marker-coverage summaries, “lack all four markers” summaries, accession/record-depth figures, family-level bar charts, family-level heatmaps, provenance summaries, provenance maps, and manuscript-ready figure exports. The R scripts therefore serve as both analysis and figure-generation scripts. A detailed inventory of all archived folders, files, and their roles in the workflow is provided in File_Index_and_Descriptions.pdf. The archive is organised to preserve the provenance of the manuscript from raw taxonomic input and repository-specific processing through to the intermediate tables, final analyses, and exported figures.
Files
Steps to reproduce
Preserve the archived folder structure after download. Install the Python dependencies listed in requirements.txt and the R packages required by the R scripts. Run the workflow sequentially: first the WoRMS harmonisation step, then the GenBank processing workflow, then the BOLD public-package processing and patching workflow, and finally the downstream R analyses in 04_Analysis Code. The R scripts use the processed GenBank and BOLD outputs to generate the manuscript summary tables, provenance outputs, and figure files. File-level details are documented in File_Index_and_Descriptions.pdf.
Institutions
- Mindanao State University NaawanNorthern Mindanao, Naawan