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Genome

Summary Table

NAME CATEGORY CITATION YEAR
CHM13 Genome Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., ... & Phillippy, A. M. (2022). The complete sequence of a human genome. Science, 376(6588), 44-53. NA
GRCh37.p13 Genome NA NA
GRCh38.p14 Genome NA NA
GRCh39 (indefinitely postponed) Genome NA NA
b37 Genome NA NA
b38 Genome NA NA
hg19 Genome NA NA
hg38 Genome NA NA
hs37d5 Genome NA NA
humanG1Kv37 Genome NA NA
CPC Pangenome Gao Y, Yang X, Chen H, Tan X, ...&, Xu S. (2023) A pangenome reference of 36 Chinese populations Nature, () . doi:10.1038/s41586-023-06173-7. PMID 37316654 2023
First draft Pangenome Liao WW, Asri M, Ebler J, Doerr D, ...&, Paten B. (2023) A draft human pangenome reference Nature, 617 (7960) 312-324. doi:10.1038/s41586-023-05896-x. PMID 37165242 2023

Genome

CHM13

  • NAME : CHM13
  • URL : https://github.com/marbl/CHM13
  • DESCRIPTION : chr1-22(CHM13),chrX(CHM13),chrY(NA24385),chrM(CHM13)
  • CITATION : Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., ... & Phillippy, A. M. (2022). The complete sequence of a human genome. Science, 376(6588), 44-53.

GRCh37.p13

  • NAME : GRCh37.p13

GRCh38.p14

GRCh39 (indefinitely postponed)

b37

b38

  • NAME : b38

hg19

  • NAME : hg19
  • URL : http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/
  • DESCRIPTION : chr1...22,chrX,chrY,chrM, unlocalized sequences (chr1_gl000191_random ...), unplaced sequences(chrUn_gl000221 ...), alternate loci (chr6_apd_hap1), chrM / chrMT (GRCh37 version / older version)

hg38

hs37d5

  • NAME : hs37d5
  • DESCRIPTION : b37: 1...22,X,Y,MT, unlocalized sequences (GL000191.1 ...), unplaced sequences(GL000211.1 ...) , NC_007605 A "decoy" sequence derived from HuRef, human BAC and Fosmid clones, and NA12878 (named "hs37d5").

humanG1Kv37

Pangenome

CPC

  • NAME : CPC
  • URL : https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA011422
  • DESCRIPTION : a collection of 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority Chinese ethnic groups.
  • TITLE : A pangenome reference of 36 Chinese populations
  • DOI : 10.1038/s41586-023-06173-7
  • ABSTRACT : Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to a pangenome form, but populations of Asian ancestry are underrepresented. Here we present data from the first phase of the Chinese Pangenome Consortium, including a collection of 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority Chinese ethnic groups. With an average 30.65× high-fidelity long-read sequence coverage, an average contiguity N50 of more than 35.63 megabases and an average total size of 3.01 gigabases, the CPC core assemblies add 189 million base pairs of euchromatic polymorphic sequences and 1,367 protein-coding gene duplications to GRCh38. We identified 15.9 million small variants and 78,072 structural variants, of which 5.9 million small variants and 34,223 structural variants were not reported in a recently released pangenome reference1. The Chinese Pangenome Consortium data demonstrate a remarkable increase in the discovery of novel and missing sequences when individuals are included from underrepresented minority ethnic groups. The missing reference sequences were enriched with archaic-derived alleles and genes that confer essential functions related to keratinization, response to ultraviolet radiation, DNA repair, immunological responses and lifespan, implying great potential for shedding new light on human evolution and recovering missing heritability in complex disease mapping.
  • CITATION : Gao Y, Yang X, Chen H, Tan X, ...&, Xu S. (2023) A pangenome reference of 36 Chinese populations Nature, () . doi:10.1038/s41586-023-06173-7. PMID 37316654
  • JOURNAL_INFO : Nature ; Nature ; 2023 ; ; ;
  • PUBMED_LINK : 37316654

First draft

  • NAME : First draft
  • URL : https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html
  • DESCRIPTION : 47 phased, diploid assemblies
  • TITLE : A draft human pangenome reference
  • DOI : 10.1038/s41586-023-05896-x
  • ABSTRACT : Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.
  • COPYRIGHT : https://creativecommons.org/licenses/by/4.0
  • CITATION : Liao WW, Asri M, Ebler J, Doerr D, ...&, Paten B. (2023) A draft human pangenome reference Nature, 617 (7960) 312-324. doi:10.1038/s41586-023-05896-x. PMID 37165242
  • JOURNAL_INFO : Nature ; Nature ; 2023 ; 617 ; 7960 ; 312-324
  • PUBMED_LINK : 37165242