GIAB Benchmarking of HG002 Assemblies from HPRC Year 1 Bakeoff

Published by National Institute of Standards and Technology | National Institute of Standards and Technology | Catalog Last Checked: August 02, 2025 at 02:45 PM | Dataset Last Updated: December 20, 2021

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).

Resources

78 resources available

Resource 1

APPLICATION/PDF

Download
Resource 2

TEXT/PLAIN

Download
Resource 3

APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET

Download
Resource 4

TEXT/PLAIN

Download
Resource 5

TEXT/PLAIN

Download
Resource 6

TEXT/PLAIN

Download
Resource 7

APPLICATION/GZIP

Download
Resource 8

TEXT/PLAIN

Download
Resource 9

APPLICATION/GZIP

Download
Resource 10

TEXT/PLAIN

Download
Resource 11

APPLICATION/GZIP

Download
Resource 12

TEXT/PLAIN

Download
Resource 13

APPLICATION/GZIP

Download
Resource 14

TEXT/PLAIN

Download
Resource 15

APPLICATION/GZIP

Download
Resource 16

TEXT/PLAIN

Download
Resource 17

APPLICATION/GZIP

Download
Resource 18

TEXT/PLAIN

Download
Resource 19

APPLICATION/GZIP

Download
Resource 20

TEXT/PLAIN

Download
Resource 21

APPLICATION/GZIP

Download
Resource 22

TEXT/PLAIN

Download
Resource 23

APPLICATION/GZIP

Download
Resource 24

TEXT/PLAIN

Download
Resource 25

APPLICATION/GZIP

Download
Resource 26

TEXT/PLAIN

Download
Resource 27

APPLICATION/GZIP

Download
Resource 28

TEXT/PLAIN

Download
Resource 29

APPLICATION/GZIP

Download
Resource 30

TEXT/PLAIN

Download
Resource 31

APPLICATION/GZIP

Download
Resource 32

TEXT/PLAIN

Download
Resource 33

APPLICATION/GZIP

Download
Resource 34

TEXT/PLAIN

Download
Resource 35

APPLICATION/GZIP

Download
Resource 36

TEXT/PLAIN

Download
Resource 37

APPLICATION/GZIP

Download
Resource 38

TEXT/PLAIN

Download
Resource 39

APPLICATION/GZIP

Download
Resource 40

TEXT/PLAIN

Download
Resource 41

APPLICATION/GZIP

Download
Resource 42

TEXT/PLAIN

Download
Resource 43

APPLICATION/GZIP

Download
Resource 44

TEXT/PLAIN

Download
Resource 45

APPLICATION/GZIP

Download
Resource 46

TEXT/PLAIN

Download
Resource 47

APPLICATION/GZIP

Download
Resource 48

TEXT/PLAIN

Download
Resource 49

APPLICATION/GZIP

Download
Resource 50

TEXT/PLAIN

Download
Resource 51

APPLICATION/GZIP

Download
Resource 52

TEXT/PLAIN

Download
Resource 53

APPLICATION/GZIP

Download
Resource 54

TEXT/PLAIN

Download
Resource 55

APPLICATION/GZIP

Download
Resource 56

TEXT/PLAIN

Download
Resource 57

APPLICATION/GZIP

Download
Resource 58

TEXT/PLAIN

Download
Resource 59

APPLICATION/GZIP

Download
Resource 60

TEXT/PLAIN

Download
Resource 61

APPLICATION/GZIP

Download
Resource 62

TEXT/PLAIN

Download
Resource 63

APPLICATION/GZIP

Download
Resource 64

TEXT/PLAIN

Download
Resource 65

TEXT/CSV

Download
Resource 66

TEXT/PLAIN

Download
Resource 67

R FILE

Download
Resource 68

TEXT/PLAIN

Download
Resource 69

TEXT/PLAIN

Download
Resource 70

TEXT/PLAIN

Download
Resource 71

TEXT/PLAIN

Download
Resource 72

TEXT/PLAIN

Download
Resource 73

APPLICATION/GZIP

Download
Resource 74

APPLICATION/OCTET-STREAM

Download
Resource 75

TEXT/PLAIN

Download
Resource 76

TEXT/PLAIN

Download
Resource 77

TEXT/TAB-SEPARATED-VALUES

Download
Resource 78

TEXT/PLAIN

Download

Find Related Datasets

Search by Tags

Click any tag below to search for similar datasets

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).
distribution	[ { "mediaType": "application/pdf", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/HPRC-Assembly-Benchmarking-Summary_2021_v2.pdf" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/HPRC-Assembly-Benchmarking-Summary_2021_v2.pdf.sha256" }, { "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/HPRC-bakeoff-assemblies-for-evaluation.xlsx" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/HPRC-bakeoff-assemblies-for-evaluation.xlsx.sha256" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/README.md" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/README.md.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-HPRC.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-HPRC.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-cur.20211005.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-cur.20211005.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-v0.11.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-v0.11.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm1.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm1.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm10ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm10ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm11ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm11ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm12.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm12.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm13.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm13.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm14ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm14ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm15.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm15.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm16ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm16ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm17ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm17ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm18.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm18.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm19ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm19ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm20ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm20ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm21.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm21.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm22ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm22ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm23ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm23ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm2ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm2ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm3a.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm3a.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm3bc.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm3bc.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm4a.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm4a.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm4bc.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm4bc.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm5.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm5.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm6ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm6ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm7ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm7ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm8ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm8ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm9_05ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm9_05ab.tar.gz.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm9ab.tar.gz" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm9ab.tar.gz.sha256" }, { "mediaType": "text/csv", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/benchmarking-summary-metrics/122021_HPRC-analysis-v2_summary-metrics.csv" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/benchmarking-summary-metrics/122021_HPRC-analysis-v2_summary-metrics.csv.sha256" }, { "format": "R file", "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/benchmarking-summary-metrics/HPRC-Assembly-Benchmarking_Reported-summary-metrics.R" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/benchmarking-summary-metrics/HPRC-Assembly-Benchmarking_Reported-summary-metrics.R.sha256" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/md5_checksums.txt" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/md5_checksums.txt.sha256" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/config.yaml" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/config.yaml.sha256" }, { "mediaType": "application/gzip", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/hprc-bakeoff-giab-analysis-archive.tar.gz" }, { "mediaType": "application/octet-stream", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/hprc-bakeoff-giab-analysis-archive.tar.gz.md5" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/hprc-bakeoff-giab-analysis-archive.tar.gz.md5.sha256" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/hprc-bakeoff-giab-analysis-archive.tar.gz.sha256" }, { "mediaType": "text/tab-separated-values", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/samples_hprc_v2.tsv" }, { "mediaType": "text/plain", "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/samples_hprc_v2.tsv.sha256" } ]
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

Have questions or suggestions about this dataset? Reach out to the contact below.