A reproducible audit framework for organelle bycatch and multi-reference ambiguity in public RAD-seq archives: a benchmark in Silene latifolia

This repository provides the full reproducible research package accompanying the manuscript entitled A reproducible audit framework for organelle bycatch and multi-reference ambiguity in public RAD-seq archives: a benchmark in Silene latifolia. The study addresses a recurring but often under-reported issue in the reuse of public RAD-seq archives: reads derived from organellar genomes and reads that map ambiguously across multiple reference compartments can substantially affect downstream interpretation, yet they are frequently summarized only by a single threshold-based metric. To address this limitation, the accompanying manuscript introduces a reproducible audit framework that separates strict organelle bycatch, inclusive organelle-associated signal, and multi-reference ambiguity, while preserving provenance across mapping and summary steps. The framework is benchmarked using public Silene latifolia RAD-seq data and includes a direct comparison with a conventional one-threshold summary approach. This deposition contains the manuscript files, publication figures, supporting information tables, derived summary data, and the complete workflow used to prepare references, process paired-end and single-end reads, aggregate compartment-aware mapping counts, generate archive-level summaries, reproduce the main figures, and perform the direct comparison against the one-threshold summary. The package also includes environment specifications, software version records, citation metadata, file inventories, and SHA-256 checksums to facilitate transparent reuse and verification. Raw sequencing data analyzed in the study are available from the NCBI Sequence Read Archive (SRA), as documented in the manuscript and accompanying metadata files. This repository therefore focuses on the reproducible computational components of the study: derived tables, workflow scripts, figure-generation code, and release metadata required to inspect, reproduce, and extend the analyses presented in the manuscript. The repository is intended for researchers working with public RAD-seq datasets, organelle-associated signal in reduced-representation sequencing, and reproducible audit-oriented bioinformatic workflows. It may also serve as a practical template for archive re-evaluation studies in which compartment-specific mapping behaviour and ambiguous read assignment need to be reported explicitly rather than collapsed into a single summary value.