학술논문
A strategy for building and using a human reference pangenome [version 1; peer review: 1 approved, 1 approved with reservations]
Document Type
software-tool
Author
Bastien Llamas; Giuseppe Narzisi; Valerie Schneider; Peter A. Audano; Evan Biederstedt; Lon Blauvelt; Peter Bradbury; Xian Chang; Chen-Shan Chin; Arkarachai Fungtammasan; Wayne E. Clarke; Alan Cleary; Jana Ebler; Jordan Eizenga; Jonas A. Sibbesen; Charles J. Markello; Erik Garrison; Shilpa Garg; Glenn Hickey; Gerard R. Lazo; Michael F. Lin; Medhat Mahmoud; Tobias Marschall; Ilia Minkin; Jean Monlong; Rajeeva L. Musunuri; Sagayamary Sagayaradj; Adam M. Novak; Mikko Rautiainen; Allison Regier; Fritz J. Sedlazeck; Jouni Siren; Yassine Souilmi; Justin Wagner; Travis Wrightsman; Toshiyuki T. Yokoyama; Qiandong Zeng; Justin M. Zook; Benedict Paten; Ben Busby
Source
F1000Research. 8:1751
Subject
Language
ISSN
2046-1402
Abstract
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.