The design and construction of reference pangenome graphs with minigraph-Reference-Cited by-同舟云学术

The design and construction of reference pangenome graphs with minigraph

Published:2020-10-16 Issue:1 Volume:21 Page:
ISSN:1474-760X
Container-title:Genome Biology
language:en
Short-container-title:Genome Biol

Author:

Li Heng^ORCID,Feng Xiaowen,Chu Chong

Abstract

AbstractThe 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.

Publisher

Springer Science and Business Media LLC

Link

https://link.springer.com/content/pdf/10.1186/s13059-020-02168-z.pdf

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