Benchmark dataset and analysis scripts for OrganelleCleaner: identification and removal of organellar contigs in genome assemblies

This dataset contains benchmark data and analysis scripts associated with the manuscript "OrganelleCleaner: identification and removal of organellar contigs in genome assemblies using graph topology, sequence features, and homology evidence" (Jeon and Kim, 2026). The dataset includes: (1) plastid and mitochondrial reference sequences for 11 plant species assembled using HiMT; (2) OrganelleCleaner classification outputs (report.tsv) for all species across three filtering modes (graph-only, BLAST-only, and hybrid); (3) input and output files for the Vitis vinifera Hi-C scaffolding validation; and (4) Python and shell scripts used to generate all figures and analyses reported in the manuscript. Raw PacBio HiFi sequencing data are publicly available at NCBI SRA and CNCB under the accession numbers listed in the README file.本数据集包含与论文《OrganelleCleaner：基于图拓扑、序列特征及同源性证据识别并去除基因组组装中的细胞器序列片段》（Jeon与Kim，2026）相关的基准测试数据与分析脚本。 本数据集包含如下内容：(1) 采用HiMT组装的11种植物的质体与线粒体参考序列；(2) 三种过滤模式（仅图分析、仅BLAST、混合模式）下所有物种的细胞器清理工具（OrganelleCleaner）分类输出结果（report.tsv）；(3) 用于葡萄（Vitis vinifera）Hi-C挂载验证的输入与输出文件；(4) 用于生成论文中所有图表与分析结果的Python及Shell脚本。 原始PacBio HiFi测序数据可在NCBI SRA与CNCB公开获取，具体登录号详见README文件。