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Contents

  • CHM13
  • GRCh39 (indefinitely postponed)
  • GRCh38
  • hg38
  • GRCh37
  • hg19
  • hs37d5
  • humanG1Kv37
  • b37
  • HUMAN PANGENOME REFERENCE CONSORTIUM
  • 1000 Genome Project 30X high coverage (hg38)
  • 1000 Genome Project Phase 3 (hg19)
  • HAPMAP3

CHM13

  • URL: https://github.com/marbl/CHM13
  • CONTENTS: 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.

GRCh39 (indefinitely postponed)

  • GRCh39 : The GRC remains committed to its mission to improve the human reference genome assembly, correcting errors and adding sequence to ensure it provides the best representation of the human genome to meet basic and clinical research needs. We will continue to make these updates publicly available at regular intervals in the form of patch releases, but have decided to indefinitely postpone our next coordinate-changing update (GRCh39) while we evaluate new models and sequence content from ongoing efforts to better represent the genetic diversity of the human pangenome, including those of the Telemore-to-Telomere Consortium and the Human Pangenome Reference Consortium.
  • url : https://www.ncbi.nlm.nih.gov/grc

GRCh38

  • SOURCE:GRC
  • DESCRIPTION: GRCh38.p14
  • URL:https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.40

hg38

  • SOURCE: UCSC
  • URL: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/

GRCh37

  • SOURCE:GRC
  • DESCRIPTION:GRCh37.p13.genome.fasta
  • URL:https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25

hg19

  • SOURCE: UCSC
  • URL : http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/
  • CONTENTS: 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)

hs37d5

  • FILE NAME: hs37d5.fa
  • SOURCE: Broad Institute, the 1000 Genomes Project Phase II
  • CONTENTS:
  • 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

  • FILE NAME: human_g1k_v37.fasta
  • SOURCE: the 1000 Genomes Project Phase I and III, Broad Institute
  • URL : http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/
  • CONTENTS: 1...22,X,Y,MT, unlocalized sequences (GL000191.1 ...), unplaced sequences(GL000211.1 ...)
  • DESCRIPTION: no haplotype sequence or EBV
  • DESCRIPTION URL: https://www.internationalgenome.org/category/assembly

b37

  • FILE NAME: Homo_sapiens_assembly19.fasta
  • SOURCE: the 1000 Genomes Project Phase I and III, Broad Institute
  • URL : https://data.broadinstitute.org/snowman/hg19/
  • CONTENTS: 1...22,X,Y,MT, unlocalized sequences (GL000191.1 ...), unplaced sequences(GL000211.1 ...) , NC_007605
  • DESCRIPTION URL:

HUMAN PANGENOME REFERENCE CONSORTIUM

  • URL:https://humanpangenome.org/data-and-resources/
  • URL:https://github.com/human-pangenomics/hpp_pangenome_resources
  • CITATION: Liao, W. W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., ... & Human Pangenome Reference Consortium. (2022). A draft human pangenome reference. bioRxiv.

1000 Genome Project - 30X high coverage

  • URL: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/
  • CITATION:Byrska-Bishop, M., Evani, U. S., Zhao, X., Basile, A. O., Abel, H. J., Regier, A. A., ... & Zody, M. C. (2022). High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell, 185(18), 3426-3440.

1000 Genome Project - Phase 3

  • URL: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
  • CITATION:1000 Genomes Project Consortium. (2015). A global reference for human genetic variation. Nature, 526(7571), 68.

HAPMAP3