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.