Supporting Data for: Assessment of Single-Nucleotide Variant Detection Strategies in the Green Sea Turtle (Chelonia mydas) for Conservation Genomics Applications

This Zenodo repository contains all processed single-nucleotide variant (SNV) call files, the assembly-derived SNV truth set, and supporting genomic resources generated in the study: “Assessment of Single-Nucleotide Variant Detection Strategies in the Green Sea Turtle (Chelonia mydas) for Conservation Genomics Applications.” The dataset includes SNV call sets produced using five variant calling tools DeepVariant, GATK HaplotypeCaller, FreeBayes, VarScan, and BCFtools along with their corresponding TABIX index files. An assembly-derived SNV truth set, generated through minimap2 alignment and bcftools normalization, is provided for benchmarking purposes. To ensure full reproducibility, the POLCA-corrected ABySS de novo genome assembly used for truth-set construction is also included. These resources enable complete replication of the SNV benchmarking analyses and facilitate transparent evaluation of variant detection performance in a non-model marine vertebrate species. 📦 Repository Contents SNV VCF files (DeepVariant, GATK, FreeBayes, VarScan, BCFtools) TABIX index files (.tbi) Assembly-derived SNV truth set (minimap2-aligned and bcftools-normalized VCF) POLCA-corrected ABySS de novo assembly (FASTA format)