biostudies-literatureUnknownHansen NFNIDA NIH HHSNHGRI NIH HHSNINDS NIH HHSNIH HHSNIGMS NIH HHSHuman genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the genome unmapped. Consequently, existing variant benchmarks, generated by the same methods, fail to assess these complex regions. To address this limitation, we present a telomere-to-telomere genome benchmark that achieves near-perfect accuracy (i.e. no detectable errors) across 99.4% of the complete, diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), totaling 15.3% of the genome that was absent from prior benchmarks. We also provide a diploid annotation of genes, transposable elements, segmental bioRxiv : the preprint server for biology2025.09.21.677443https://www.ebi.ac.uk/biostudies/studies/S-EPMC12458380biostudies-literatureA complete diploid human genome benchmark for personalized genomics.PMC12458380R35 GM156470U24 HG010263U01 HG011758UM1 HG010971R01 HG011274K99 GM155552U01 HG013744R00 GM147352R01 HG010169UM1 DA058220T32 GM007454R01 HG006677UG3 NS132105DP5 OD029630UM1 DA058229R35 GM130151Asri MAntipov DO'Neill RJRiethman HCarroll AStergachis ABAdam ELogsdon GABarreira SLipovac JSikic MSolar SJJi HJOshima KKRautiainen MChu YStorer JMAltemose NWagner JKang YCarioscia SAGuarracino AVollger MRShafin KNegi SEbert PFleharty MFleming LEJenike KSedlazeck FJFormenti GBzikadze AVSchnabel RDYoo DRanjan DSweeten APMastoras MSchatz MCRhie AKim JHansen NFKalleberg JKoren SBohaczuk SCPickett BDSalzberg SLPaulin LFKing RRanchalis JMiga KHPorubsky DMitchell MWGarrison EOlson NDDwarshuis NChao KHEnglish AZhou YPhillippy AMHartley GALoucks HEichler EEZook JMDas ATimp WfalseA complete diploid human genome benchmark for personalized genomics.Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the genome unmapped. Consequently, existing variant benchmarks, generated by the same methods, fail to assess these complex regions. To address this limitation, we present a telomere-to-telomere genome benchmark that achieves near-perfect accuracy (i.e. no detectable errors) across 99.4% of the complete, diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), totaling 15.3% of the genome that was absent from prior benchmarks. We also provide a diploid annotation of genes, transposable elements, segmental 2025-01-01T00:00:00Z2025 Sep2026-05-04T03:22:44.817Z2026-05-04T03:14:18.689ZS-EPMC124583804100095310.1101/2025.09.21.677443