The design and construction of reference pangenome graphs with minigraph

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...

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Bibliographic Details
Published inGenome Biology Vol. 21; no. 1; p. 265
Main Authors Li, Heng, Feng, Xiaowen, Chu, Chong
Format Journal Article
LanguageEnglish
Published England BioMed Central 16.10.2020
BMC
Subjects
Animals
Bioinformatics
Chromosomes
Genetic diversity
Genome, Human
Genomes
Genomic Structural Variation
Genomics
Genomics - methods
Genomics - standards
Haplotypes
Humans
Method
Pangenome
Reference Standards
Pangenome
Bioinformatics
Genomics
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Summary: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.
Bibliography:ObjectType-Article-2
SourceType-Scholarly Journals-1
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-020-02168-z