Channel: Human Pangenome Reference Consortium (HPRC)

bioRxiv posts many COVID19-related papers. A reminder: they have not been formally peer-reviewed and should not guide health-related behavior or be reported in the press as conclusive.

94 Articles

Local read haplotagging enables accurate long-read small variant calling

Kolesnikov, A., Cook, D. E., Nattestad, M., Ashley, E. A., Gorzynski, J., Goenka, S. D., Jain, M., McNulty, B., Miga, K. H., Paten, B., Chang, P.-C., Carroll, A., Shafin, K.

10.1101/2023.09.07.556731 — Posted: 2023-09-12

Regulatory Transposable Elements in the Encyclopedia of DNA Elements

Du, A. Y., Chobirko, J. D., Zhuo, X., Feschotte, C., Wang, T.

10.1101/2023.09.05.556380 — Posted: 2023-09-06

The complete sequence of a human Y chromosome

Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., Allen, J., Asri, M., Bzikadze, A. V., Chen, N.-C., Chin, C.-S., Diekhans, M., Flicek, P., Formenti, G., Fungtammasan, A., Garcia Giron, C., Garrison, E., Gershman, A., Gerton, J., Grady, P. G., Guarracino, A., Haggerty, L., Halabian, R., Hansen, N. F., Harris, R., Hartley, G. A., Harvey, W. T., Haukness, M., Heinz, J., Hourlier, T., Hubley, R. M., Hunt, S. E., Hwang, S., Jain, M., Kesharwani, R. K., Lewis, A. P., Li, H., Logsdon, G. A., Lucas, J. K., Makalowski

10.1101/2022.12.01.518724 — Posted: 2023-07-11

Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation

Hallast, P., Ebert, P., Loftus, M., Yilmaz, F., Audano, P. A., Logsdon, G. A., Bonder, M. J., Zhou, W., Hoeps, W., Kim, K., Li, C., Hoyt, S. J., Dishuck, P. C., Porubsky, D., Tsetsos, F., Kwon, J. Y., Zhu, Q., Munson, K. M., Hasenfeld, P., Harvey, W. T., Lewis, A. P., Kordosky, J., Hoekzema, K., (HGSVC), T. H. G. S. V. C., O'Neill, R. J., Korbel, J. O., Tyler-Smith, C., Eichler, E. E., Shi, X., Beck, C. R., Marschall, T., Konkel, M. K., Lee, C.

10.1101/2022.12.01.518658 — Posted: 2023-06-12

Evaluation of haplotype-aware long-read error correction with hifieval

Guo, Y., Feng, X., Li, H.

10.1101/2023.06.05.543788 — Posted: 2023-06-07

A comprehensive catalog of 3D genome organization in diverse human genomes facilitates understanding of the impact of structural variation on chromatin structure

Li, C., Bonder, M. J., Syed, S., Human Genome Structural Variation Consortium (HGSVC), , HGSVC Functional Analysis Working Group, , Zody, M. C., Chaisson, M. J. P., Talkowski, M. E., Marschall, T., Korbel, J. O., Eichler, E. E., Lee, C., Shi, X.

10.1101/2023.05.15.540856 — Posted: 2023-05-15

Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall

Harvey, W. T., Ebert, P., Ebler, J., Audano, P. A., Munson, K. M., Hoekzema, K., Porubsky, D. E., Beck, C. R., Marschall, T. R., Garimella, K. V., Eichler, E. E.

10.1101/2023.05.04.539448 — Posted: 2023-05-04

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

Hickey, G., Monlong, J., Ebler, J., Novak, A., Eizenga, J. M., Gao, Y., Human Pangenome Reference Consortium, , Marschall, T., Li, H., Paten, B.

10.1101/2022.10.06.511217 — Posted: 2023-04-12

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

Kolmogorov, M., Billingsley, K. J., Mastoras, M., Meredith, M., Monlong, J., Lorig-Roach, R., Asri, M., Alvarez Jerez, P., Malik, L., Dewan, R., Reed, X., Genner, R. M., Daida, K., Behera, S., Shafin, K., Pesout, T., Prabakaran, J., Carnevali, P., North American Brain Expression Consortium (NABEC), , Yang, J., Rhie, A., Scholz, S. W., Traynor, B. J., Miga, K. H., Jain, M., Timp, W., Phillippy, A. M., Chaisson, M., Sedlazeck, F. J., Blauwendraat, C., Paten, B.

10.1101/2023.01.12.523790 — Posted: 2023-04-05

Evolutionary constraint and innovation across hundreds of placental mammals

Christmas, M. J., Kaplow, I. M., Genereux, D. P., Dong, M. X., Hughes, G. M., Li, X., Sullivan, P. F., Hindle, A. G., Andrews, G., Armstrong, J. C., Bianchi, M., Breit, A. M., Diekhans, M., Fanter, C., Foley, N. M., Goodman, D. B., Goodman, L., Keough, K. C., Kirilenko, B., Kowalczyk, A., Lawless, C., Lind, A. L., Meadows, J. R. S., Moreira, L. R., Redlich, R. W., Ryan, L., Swofford, R., Valenzuela, A., Wagner, F., Wallerman, O., Brown, A. R., Damas, J., Fan, K., Gatesy, J., Grimshaw, J., Johnson, J., Kozyrev, S. V., Lawler, A. J., Marinescu, V. D., Morrill, K. M., Osmanski, A., Paulat, N. S.

10.1101/2023.03.09.531574 — Posted: 2023-03-09

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