The design and construction of reference pangenome graphs with minigraph
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 propos...
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2020-10-01
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| Series: | Genome Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s13059-020-02168-z |
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doaj-70e3bfefab6a479999dc7cc28f1a76402020-11-25T04:08:11ZengBMCGenome Biology1474-760X2020-10-0121111910.1186/s13059-020-02168-zThe design and construction of reference pangenome graphs with minigraphHeng Li0Xiaowen Feng1Chong Chu2Department of Data Sciences, Dana-Farber Cancer InstituteDepartment of Data Sciences, Dana-Farber Cancer InstituteDepartment of Biomedical Informatics, Harvard Medical SchoolAbstract 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.http://link.springer.com/article/10.1186/s13059-020-02168-zBioinformaticsGenomicsPangenome |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Heng Li Xiaowen Feng Chong Chu |
| spellingShingle |
Heng Li Xiaowen Feng Chong Chu The design and construction of reference pangenome graphs with minigraph Genome Biology Bioinformatics Genomics Pangenome |
| author_facet |
Heng Li Xiaowen Feng Chong Chu |
| author_sort |
Heng Li |
| title |
The design and construction of reference pangenome graphs with minigraph |
| title_short |
The design and construction of reference pangenome graphs with minigraph |
| title_full |
The design and construction of reference pangenome graphs with minigraph |
| title_fullStr |
The design and construction of reference pangenome graphs with minigraph |
| title_full_unstemmed |
The design and construction of reference pangenome graphs with minigraph |
| title_sort |
design and construction of reference pangenome graphs with minigraph |
| publisher |
BMC |
| series |
Genome Biology |
| issn |
1474-760X |
| publishDate |
2020-10-01 |
| description |
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. |
| topic |
Bioinformatics Genomics Pangenome |
| url |
http://link.springer.com/article/10.1186/s13059-020-02168-z |
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AT hengli thedesignandconstructionofreferencepangenomegraphswithminigraph AT xiaowenfeng thedesignandconstructionofreferencepangenomegraphswithminigraph AT chongchu thedesignandconstructionofreferencepangenomegraphswithminigraph AT hengli designandconstructionofreferencepangenomegraphswithminigraph AT xiaowenfeng designandconstructionofreferencepangenomegraphswithminigraph AT chongchu designandconstructionofreferencepangenomegraphswithminigraph |
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