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Table 1 Third-generation sequencing initiatives and reference data sets

From: Computational methods for chromosome-scale haplotype reconstruction

Initiatives # samples/#haplotypes Technologies Links
Genome in a Bottle [17, 18] (GIAB) 2 trios and 1 sample, 6 haplotypes PacBio, ONT, Illumina, BioNano, Strand-seq, 10xG ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/
Human Genome Structural Variation Consortium [15] (HGSVC) > 3 trios, > 6 haplotypes PacBio, Illumina, BioNano, Hi-C, Strand-seq, 10xG https://www.internationalgenome.org/data
Vertebrate Genome Project (VGP; facilitated by Genome 10 K), Darwin Tree of Life Project > 100, ongoing haplotyping efforts 10xG, PacBio, Hi-C https://vgp.github.io/genomeark/
Human Pangenome Project > 10, > 20 haplotypes PacBio, ONT, Hi-C https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=HPRC/
Earth Biogenome Project (facilitated by Genome 10 K) > 10, ongoing haplotyping efforts PacBio, Hi-C https://www.earthbiogenome.org/publications
The DNA Zoo project > 10, ongoing haplotyping efforts Hi-C and WGS https://www.dnazoo.org/
Japanese Reference Project [19] (1KJPN) > 1, > 2 haplotypes PacBio, Illumina https://jrg.megabank.tohoku.ac.jp/en
CHM1, CHM13 [20], HX1 [21], PGP-1 [22], AK1 [23] Individual samples, two haplotypes each (except CHM1 and CHM13) PacBio, ONT, BioNano, Hi-C, Illumina n/a