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The Genome In A Bottle HG002 assembly-based variant benchmark set enables comprehensive benchmarking of small and structural variants

Nathan D. Olson Nathan Dwarshuis Nancy F. Hansen S. Koren A. Rhie Jennifer H. McDaniel Justin Wagner G. Berry Kishwar Shafin A. English Christopher T. Saunders Ritu Kundu James M. Holt Donald Freed Adetola A. Abdulkadir Camille A. Daniels Sina Majidian L. Paulin F. Sedlazeck M. Fleharty Yue-Yao Gao Luca Denti Lucas Brambrink Andrew Carroll Pi-Chuan Chang Daniel E. Cook Alexey Kolesnikov S. Catreux Christopher Edlund James Han Lisa Murray Yu-Tong Qiu Massimiliano Rossi Konrad Scheffler S. Truong Yi-Na Wang R. Chikhi C. Flores D. Jáspez J. Lorenzo-Salazar A. Muñoz-Barrera L. A. Rubio-Rodríguez Mao-Jan Lin Kavya Vaddadi B. Langmead Chun-Lin Xiao Sean Mckenzie Jonathan R. Belyeu M. Eberle Z. Kronenberg Juniper A. Lake William J. Rowell Aaron M. Wenger S. M. Sahraeian Omer Barad Hila Benjamin Ilya Soifer F. Hormozdiari M. F. Mootor Y. Patel T. Yamaguchi P. Bonizzoni P. Boutros A. Phillippy J. Zook
Sep 2026 · bioRxiv · 1 citation · 54 references
Biology

TL;DR

The Genome in a Bottle (GIAB) Consortium’s HG002 v5.0q benchmark set is presented, a more comprehensive variant benchmark derived from a fully phased, highly curated, and accurate diploid assembly of HG002 to provide confident small- and structural-variant calls across previously inaccessible regions.

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