GIAB Benchmarking of HG002 Assemblies from HPRC Year 1 Bakeoff

Published by National Institute of Standards and Technology | National Institute of Standards and Technology | Metadata Last Checked: June 27, 2025 | Last Modified: 2021-12-20 00:00:00

The Human Pangenome Reference Consortium (HPRC) tested which combination of current genome sequencing and automated assembly approaches yields the most complete, accurate, and cost-effective diploid genome assemblies with minimal manual curation. Assemblies were generated for GIAB HG002. Variant calls from twenty-nine assemblies were evaluated by NIST using dipcall v0.3 (https://github.com/lh3/dipcall) to produce variant calls when aligned to GRCh38. Benchmarking of small variant calls was then performed against GIAB benchmark v4.2.1 using hap.py v3.12 (https://github.com/Illumina/hap.py).

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Human genomics; DNA sequencing; Reference materials; genome assembly; variant calling; benchmarking; HG002; HPRC

Complete Metadata

bureauCode	[ "006:55" ]
identifier	ark:/88434/mds2-2578
landingPage	https://data.nist.gov/od/id/mds2-2578
language	[ "en" ]
programCode	[ "006:045" ]
references	[ "https://doi.org/10.1101/2022.03.06.483034" ]
rights	The assemblies provided by Human Pangenome Reference Consortium (HPRC) for evaluation were generated by the HPRC, and its data use protocol is at https://humanpangenome.org/data-use-protocol/
theme	[ "Bioscience:Genomic measurements" ]