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 |