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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: August 02, 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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Complete Metadata
@type dcat:Dataset
accessLevel public
accrualPeriodicity irregular
bureauCode 
                                            [
  "006:55"
]
contactPoint 
                                            {
  "fn": "Justin Zook",
  "hasEmail": "mailto:justin.zook@nist.gov"
}
description 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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identifier ark:/88434/mds2-2578
keyword 
                                            [
  "Human genomics; DNA sequencing; Reference materials;  genome assembly; variant calling; benchmarking; HG002; HPRC"
]
landingPage https://data.nist.gov/od/id/mds2-2578
language 
                                            [
  "en"
]
license https://www.nist.gov/open/license
modified 2021-12-20 00:00:00
programCode 
                                            [
  "006:045"
]
publisher 
                                            {
  "name": "National Institute of Standards and Technology",
  "@type": "org:Organization"
}
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"
]
title GIAB Benchmarking of HG002 Assemblies from HPRC Year 1 Bakeoff

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