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The design and construction of reference pangenome graphs with minigraph

Authors
  • Li, Heng1, 2
  • Feng, Xiaowen1, 2
  • Chu, Chong2
  • 1 Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA , Boston (United States)
  • 2 Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02215, USA , Boston (United States)
Type
Published Article
Publication Date
Oct 16, 2020
Volume
21
Issue
1
Identifiers
DOI: 10.1186/s13059-020-02168-z
Source
Springer Nature
Keywords
License
Green

Abstract

The recent advances in sequencing technologies enable the assembly of individual genomes to the quality of the reference genome. How to integrate multiple genomes from the same species and make the integrated representation accessible to biologists remains an open challenge. Here, we propose a graph-based data model and associated formats to represent multiple genomes while preserving the coordinate of the linear reference genome. We implement our ideas in the minigraph toolkit and demonstrate that we can efficiently construct a pangenome graph and compactly encode tens of thousands of structural variants missing from the current reference genome.

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