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)本Zenodo仓储收纳了本研究生成的全部经过预处理的单核苷酸变异（single-nucleotide variant, SNV）调用文件、基于基因组组装得到的SNV真值集，以及配套的基因组学资源。本研究的主题为《面向保护基因组学应用的绿海龟（Chelonia mydas）单核苷酸变异检测策略评估》。 本数据集涵盖由5款变异检测工具生成的SNV调用集，分别为DeepVariant、GATK HaplotypeCaller、FreeBayes、VarScan及BCFtools，同时附带各工具对应结果的TABIX索引文件。此外，为满足基准测试需求，本数据集还提供了通过minimap2比对与bcftools标准化流程构建的组装来源SNV真值集。 为保障研究可完全复现，本数据集同时收录了用于构建该真值集的、经POLCA校正的ABySS从头组装基因组。 这些资源可实现单核苷酸变异基准测试分析的完整复现，并支持对非模式海洋脊椎动物物种的变异检测性能开展透明化评估。 📦 仓储内容 SNV VCF文件（包含DeepVariant、GATK、FreeBayes、VarScan、BCFtools的变异检测结果） TABIX索引文件（文件后缀为.tbi） 基于组装得到的SNV真值集（经minimap2比对与bcftools标准化处理的VCF格式文件） 经POLCA校正的ABySS从头组装基因组（FASTA格式）