Data provided by National Institute of Standards and Technology
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).
About this Dataset
Updated: 2025-04-06
Metadata Last Updated:
2021-12-20 00:00:00
Date Created:
N/A
Data Provided by:
Dataset Owner:
N/A
| Title | GIAB Benchmarking of HG002 Assemblies from HPRC Year 1 Bakeoff |
|---|---|
| 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). |
| Modified | 2021-12-20 00:00:00 |
| Publisher Name | National Institute of Standards and Technology |
| Contact | mailto:[email protected] |
| Keywords | Human genomics; DNA sequencing; Reference materials; genome assembly; variant calling; benchmarking; HG002; HPRC |
{
"identifier": "ark:\/88434\/mds2-2578",
"accessLevel": "public",
"contactPoint": {
"hasEmail": "mailto:[email protected]",
"fn": "Justin Zook"
},
"programCode": [
"006:045"
],
"landingPage": "https:\/\/data.nist.gov\/od\/id\/mds2-2578",
"title": "GIAB Benchmarking of HG002 Assemblies from HPRC Year 1 Bakeoff",
"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).",
"language": [
"en"
],
"distribution": [
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/snakemake-pipeline\/config.yaml.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/snakemake-pipeline\/samples_hprc_v2.tsv",
"mediaType": "text\/tab-separated-values"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/snakemake-pipeline\/samples_hprc_v2.tsv.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/snakemake-pipeline\/hprc-bakeoff-giab-analysis-archive.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/snakemake-pipeline\/hprc-bakeoff-giab-analysis-archive.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/snakemake-pipeline\/hprc-bakeoff-giab-analysis-archive.tar.gz.md5",
"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.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/README.md.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\/HPRC-bakeoff-assemblies-for-evaluation.xlsx",
"mediaType": "application\/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
},
{
"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\/HPRC-Assembly-Benchmarking-Summary_2021_v2.pdf",
"mediaType": "application\/pdf"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/HPRC-Assembly-Benchmarking-Summary_2021_v2.pdf.sha256",
"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\/benchmarking-summary-metrics\/122021_HPRC-analysis-v2_summary-metrics.csv",
"mediaType": "text\/csv"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/benchmarking-summary-metrics\/122021_HPRC-analysis-v2_summary-metrics.csv.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm22ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm22ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm6ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm6ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm14ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm14ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm11ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm11ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm10ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm10ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm2ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm2ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm7ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm7ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/HG002-cur.20211005.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/HG002-cur.20211005.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/HG002-HPRC.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/HG002-HPRC.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm17ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm17ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm23ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm23ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/HG002-v0.11.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/HG002-v0.11.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm9_05ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm9_05ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm9ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm9ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm4bc.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm4bc.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm19ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm19ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm1.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm1.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm3bc.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm3bc.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm15.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm15.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm20ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm20ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm8ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm8ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm12.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm12.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm18.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm18.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm21.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm21.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm5.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm5.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm16ab.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm16ab.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm3a.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm3a.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm4a.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm4a.tar.gz.sha256",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm13.tar.gz",
"mediaType": "application\/gzip"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/assemblies-and-benchmarking_results\/asm13.tar.gz.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\/README.md",
"mediaType": "text\/plain"
},
{
"downloadURL": "https:\/\/data.nist.gov\/od\/ds\/ark:\/88434\/mds2-2578\/benchmarking-summary-metrics\/HPRC-Assembly-Benchmarking_Reported-summary-metrics.R",
"format": "R file",
"mediaType": "text\/plain"
}
],
"bureauCode": [
"006:55"
],
"modified": "2021-12-20 00:00:00",
"publisher": {
"@type": "org:Organization",
"name": "National Institute of Standards and Technology"
},
"theme": [
"Bioscience:Genomic measurements"
],
"keyword": [
"Human genomics; DNA sequencing; Reference materials; genome assembly; variant calling; benchmarking; HG002; HPRC"
]
}
