A strategy for building and using a human reference pangenome.

TitleA strategy for building and using a human reference pangenome.
Publication TypeJournal Article
Year of Publication2019
AuthorsLlamas, B, Narzisi, G, Schneider, V, Audano, PA, Biederstedt, E, Blauvelt, L, Bradbury, P, Chang, X, Chin, C-S, Fungtammasan, A, Clarke, WE, Cleary, A, Ebler, J, Eizenga, J, Sibbesen, JA, Markello, CJ, Garrison, E, Garg, S, Hickey, G, Lazo, GR, Lin, MF, Mahmoud, M, Marschall, T, Minkin, I, Monlong, J, Musunuri, RL, Sagayaradj, S, Novak, AM, Rautiainen, M, Regier, A, Sedlazeck, FJ, Siren, J, Souilmi, Y, Wagner, J, Wrightsman, T, Yokoyama, TT, Zeng, Q, Zook, JM, Paten, B, Busby, B
Date Published2019

In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.

Alternate JournalF1000Res
PubMed ID34386196
PubMed Central IDPMC8350888
Grant ListU41 HG007234 / HG / NHGRI NIH HHS / United States
UM1 HG008898 / HG / NHGRI NIH HHS / United States