SVScope improves somatic structural variations detection via graph-genome optimization (Source Code)

This dataset provides a persistent archive of the SVScope pipeline, including its source code, demonstration materials, and the specific analysis scripts used to generate the results presented in our Genome Biology manuscript: "SVScope improves somatic structural variations detection via graph-genome optimization". SVScope is a comprehensive tool designed for the precise detection and visualization of somatic structural variations (SVs) from long-read sequencing data. File Descriptions: Demo_reference_SourceCode.tar.gz: SVScope Source Code: The core implementation of the SVScope algorithm. Demo Data: Sample BAM files (from PacBio and ONT platforms) and test datasets to allow for immediate validation of the pipeline's functionality. Reference Genome: The specific reference genome sequences (e.g., hg38/GRCh38) and index files used for the local graph-genome optimization process described in the paper. CodeForThisPaper.tar.gz: A collection of custom scripts used for benchmarking, data processing, and performance evaluation. Update log: v4.0 (2026-03-27): Add --verbose parameter to suppresses running log, and fix pandas warnings in SVScope Source Code. v3.0 (2026-03-07): Fix inconsistant CPU number bug in source code. v2.0 (2026-03-07): Fix biopython application error in SVScope source code. v1.0 (2026-01-15): Initial release.本数据集提供了SVScope流程的永久存档，涵盖其源代码、演示材料，以及用于复现我们发表于《Genome Biology》的论文"SVScope improves somatic structural variations detection via graph-genome optimization"中所得结果的专属分析脚本。SVScope是一款专为从长读长测序数据中精准检测并可视化体细胞结构变异（somatic structural variations, SVs）而开发的综合性工具。 文件说明： Demo_reference_SourceCode.tar.gz： SVScope源代码：SVScope算法的核心实现代码。 演示数据：源自PacBio与ONT平台的示例BAM文件及测试数据集，可直接用于验证该流程的功能。 参考基因组：论文中所述局部图基因组优化流程所使用的特定参考基因组序列（如hg38/GRCh38）及索引文件。 CodeForThisPaper.tar.gz： 用于基准测试、数据处理与性能评估的自定义脚本集合。 更新日志： v4.0 (2026-03-27)：新增--verbose参数以抑制运行日志，并修复了SVScope源代码中的pandas警告问题。 v3.0 (2026-03-07)：修复了源代码中CPU数量不一致的漏洞。 v2.0 (2026-03-07)：修复了SVScope源代码中的Biopython应用错误。 v1.0 (2026-01-15)：首次正式发布。