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).

Resources

Name Format Description Link
49 samples_hprc_v2.tsv https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/samples_hprc_v2.tsv
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/samples_hprc_v2.tsv.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/hprc-bakeoff-giab-analysis-archive.tar.gz.sha256
5 hprc-bakeoff-giab-analysis-archive.tar.gz.md5 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/hprc-bakeoff-giab-analysis-archive.tar.gz.md5
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/hprc-bakeoff-giab-analysis-archive.tar.gz.md5.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/README.md.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/md5_checksums.txt.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/benchmarking-summary-metrics/HPRC-Assembly-Benchmarking_Reported-summary-metrics.R.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/benchmarking-summary-metrics/122021_HPRC-analysis-v2_summary-metrics.csv.sha256
19 asm22ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm22ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm6ab.tar.gz.sha256
19 asm14ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm14ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm14ab.tar.gz.sha256
19 asm11ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm11ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm11ab.tar.gz.sha256
19 asm10ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm10ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm2ab.tar.gz.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm7ab.tar.gz.sha256
19 HG002-cur.20211005.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-cur.20211005.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-cur.20211005.tar.gz.sha256
19 HG002-HPRC.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-HPRC.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-HPRC.tar.gz.sha256
19 asm17ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm17ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm17ab.tar.gz.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm23ab.tar.gz.sha256
19 HG002-v0.11.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-v0.11.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/HG002-v0.11.tar.gz.sha256
19 asm9_05ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm9_05ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm1.tar.gz.sha256
19 asm3bc.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm3bc.tar.gz
19 asm15.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm15.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm15.tar.gz.sha256
19 asm20ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm20ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm12.tar.gz.sha256
19 asm18.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm18.tar.gz
19 asm21.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm21.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm21.tar.gz.sha256
19 asm5.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm5.tar.gz
19 asm16ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm16ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm16ab.tar.gz.sha256
19 asm3a.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm3a.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm4a.tar.gz.sha256
19 asm13.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm13.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm13.tar.gz.sha256
19 asm9ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm9ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm9ab.tar.gz.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm20ab.tar.gz.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm8ab.tar.gz.sha256
19 asm12.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm12.tar.gz
19 hprc-bakeoff-giab-analysis-archive.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/hprc-bakeoff-giab-analysis-archive.tar.gz
33 HPRC-Assembly-Benchmarking-Summary_2021_v2.pdf https://data.nist.gov/od/ds/ark:/88434/mds2-2578/HPRC-Assembly-Benchmarking-Summary_2021_v2.pdf
19 asm8ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm8ab.tar.gz
19 asm2ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm2ab.tar.gz
53 HPRC-bakeoff-assemblies-for-evaluation.xlsx https://data.nist.gov/od/ds/ark:/88434/mds2-2578/HPRC-bakeoff-assemblies-for-evaluation.xlsx
19 asm7ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm7ab.tar.gz
19 asm1.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm1.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm5.tar.gz.sha256
19 asm23ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm23ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm3a.tar.gz.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm22ab.tar.gz.sha256
8 122021_HPRC-analysis-v2_summary-metrics.csv https://data.nist.gov/od/ds/ark:/88434/mds2-2578/benchmarking-summary-metrics/122021_HPRC-analysis-v2_summary-metrics.csv
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm18.tar.gz.sha256
0 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/benchmarking-summary-metrics/HPRC-Assembly-Benchmarking_Reported-summary-metrics.R
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/config.yaml.sha256
47 md5_checksums.txt https://data.nist.gov/od/ds/ark:/88434/mds2-2578/md5_checksums.txt
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/HPRC-Assembly-Benchmarking-Summary_2021_v2.pdf.sha256
19 asm6ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm6ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm9_05ab.tar.gz.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm4bc.tar.gz.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm3bc.tar.gz.sha256
47 config.yaml https://data.nist.gov/od/ds/ark:/88434/mds2-2578/snakemake-pipeline/config.yaml
47 README.md https://data.nist.gov/od/ds/ark:/88434/mds2-2578/README.md
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/HPRC-bakeoff-assemblies-for-evaluation.xlsx.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm10ab.tar.gz.sha256
19 asm4bc.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm4bc.tar.gz
19 asm19ab.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm19ab.tar.gz
47 https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm19ab.tar.gz.sha256
19 asm4a.tar.gz https://data.nist.gov/od/ds/ark:/88434/mds2-2578/assemblies-and-benchmarking_results/asm4a.tar.gz

Tags

  • human-genomics-dna-sequencing-reference-materials-genome-assembly-variant-calling-benchmarking-

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