The design and construction of reference pangenome graphs with minigraph
By Heng Li, Xiaowen Feng, Chong Chu. Genome Biology, 2020
367 citations recorded by the source corpus.
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.
Subfields: Genetics, Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/4aa51fbe41e6588e59c8f9f7aaaaac3c83a56019
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Genetics
- Heng Li
- Adam M. Phillippy
- Xiaowen Feng
- Haley Abel
- Evan E. Eichler
- Kerstin Howe
- Benedict Paten
- Mark J. P. Chaisson
In Molecular Biology
- Heng Li
- Adam M. Phillippy
- Evan E. Eichler
- Benedict Paten
- Xiaowen Feng
- Mark J. P. Chaisson
- Mitchell R. Vollger
- Paul Flicek
In Plant Science
- Heng Li
- Evan E. Eichler
- David Haussler
- Benedict Paten
- Adam M. Phillippy
- Mark J. P. Chaisson
- Paul Flicek
Citations in the corpus
- A draft human pangenome reference (2022, methodology): “The SV sites were then annotated as described in the Methods section of minigraph paper (Li et al., 2020).”
- Pangenomics enables genotyping known structural variants in 5,202 diverse genomes (2021, methodology): “ForSVs,andforparticularlylargeinser-tions,weandothershaveshownthatthe benefitsofpangenomesforgenotypingare notmerelyincrementalbuttransformative ( 8 , 39 , 44 ).”
- New strategies to improve minimap2 alignment accuracy (2021, methodology): “This has inspired new chaining algorithms (Li et al., 2020; Ren and Chaisson, 2021) which are not integrated into minimap2.”