Extended Data Table 1 |.
Datasets generated and/or used in this study
| Datasets generated in this study | ||||||
|---|---|---|---|---|---|---|
| Species | Sample | Data type | BioProject | Accession # | URL | Reference |
| Human (Homo sapiens) | CHM1 | Whole-genome assembly with complete centromeres | PRJNA975207 | JASMMY000000000 | -- | This study |
| PacBio HiFi | PRJNA726974 | SRX10759865-SRX10759866 | https://s3-us-west-2.amazonaws.com/human-pangenomics/index.ht | This study | ||
| ONT | PRJNA869061 | SRX17054101-SRX17054194 | -- | This study | ||
| Strand-seq | -- | -- | https://doi.org/10.5281/zenodo.7959305 | This study | ||
| CENP-A ChlP-seq | PRJNA975217 | SRR24675260-SRR24675263 | -- | This study | ||
| HG00733 | PacBio HiFi | PRJNA975575 | SRR24707288-SRR24707292 | -- | This study | |
| ONT | PRJNA975575 | SRR24715152-SRR24715211 | -- | This study | ||
| Chimpanzee (Pan troglodytes) | Clint; S006007 | ONT | PRJNA659034 | SRR24707265-SRR24707284 | -- | This study |
| Orangutan (Pongo abelii) | Susie; PR01109 | ONT | PRJNA659034 | SRR24706432-SRR24706459 | -- | This study |
| Macaque (Macaca mulatta) | AG07107 | ONT | PRJNA659034 | SRR24709228-SRR24709293 | -- | This study |
| Previously published datasets | ||||||
| CHM1 | Illumina | PRJNA246220 | SRR1514950-SRR1514952 | -- | Chaisson et al., Nature, 2015 | |
| Human (Homo sapiens) | CHM13 | Whole-genome assembly | PRJNA559484 | GCA_009914755.4 | -- | Nurk et al., Science, 2022 |
| PacBio HiFi | PRJNA530776 | SRR11292120-SRR11292123 | -- | Nurk et al., Genome Res, 2020 | ||
| ONT | PRJNA559484 | SRR10035479-SRR10035573, SRR12564439-SRR12564459, SRR12618224-SRR12618325 | -- | Logsdon et al., Nature, 2021; Miga et al., Nature, 2020 | ||
| HG00733 | PacBio HiFi | PRJEB36100 | ERR3822935, ERR3861382-ERR3861387 | -- | Logsdon et al., Nature, 2021; Vollger et al., Nature, 2023 | |
| ONT | PRJNA686388 | SRR13356541-SRR13356542, SRR13362355-SRR13362359, SRR13362450-SRR13362451 | -- | Logsdon et al., Nature, 2021 | ||
| PRJEB37264 | ERR3988477-ERR3988509 | -- | Shafin etal., Nature Biotechnol, 2020 | |||
| HPRC (various) | Whole-genome assembly | -- | -- | https://proiects.ensembl.org/hprc/ | Liao, W.-W. et al., Nature, 2023 | |
| HGSVC (various) | Whole-genome assembly | -- | -- | https://www.intemationalgenome.org/data-portal/data-collection/hgsvc2 | Ebert et al., Science, 2021 | |
| Chimpanzee (Pan troglodytes) | Clint; S006007 | PacBio HiFi | PRJNA659034 | SRR12517369-SRR12517374, SRR12517378, SRR12517389-SRR12517390 | -- | Logsdon et al., Nature, 2021 |
| ONT | PRJNA659034 | SRR12552556-SRR12552568 | -- | Logsdon et al., Nature, 2021 | ||
| Orangutan (Pongo abelii) | Susie; PR01109 | PacBio HiFi | PRJNA659034 | SRR12517385-SRR12517387 | -- | Logsdon et al., Nature, 2021 |
| ONT | PRJNA659034 | SRR12551266-SRR12551275 | -- | Logsdon et al., Nature, 2021 | ||
| Macaque (Macaca mulatta) | AG 07107 | PacBio HiFi | PRJNA659034 | SRR12517375-SRR12517377, SRR12517379-SRR12517381 | -- | Logsdon et al., Nature, 2021 |
| ONT | PRJNA659034 | SRR12517382-SRR12517385 | -- | Logsdon et al., Nature, 2021 | ||
See accompanying Excel file. ONT, Oxford Nanopore Technologies; PacBio, Pacific Biosciences; HiFi, high-fidelity; ChIP, chromatin immunoprecipitation.