Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes. Nat. Genet. 54, 518–525 (2022). Article PubMed PubMed Central CAS Google Scholar Di Genova,
In the present study, we propose a new algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference together with-mer counts from short-read sequencing data to genotype a wide spectrum of genetic variation鈥攁 process we refer to as genome inference. Compared with mapping-based ...
Pangenome-based genome inference. Contribute to eblerjana/pangenie development by creating an account on GitHub.
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes. Nat. Genet. 54, 518–525 (2022). Article CAS PubMed PubMed Central Google Scholar Li, M.-H. & Merilä, J. Population differences in levels of linkage disequilibrium in the...
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes. Nature Genet. 2022;54:518–25. Article CAS PubMed Google Scholar Zhou Y, Yang L, Han X, Han J, Hu Y, Li F, et al. Assembly of a pangenome for global cattle reveals ...
Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 pub
However, numerous recent studies have highlighted that SV-based genome-wide association study (GWAS) analysis is an effective strategy for identifying genes involved in complex agronomic traits. For instance, loci associated with complex agronomic traits of drought resistance, early leaf senescence, ...
The grapevine (Vitis vinifera) is an economically important crop of global significance, cultivated across the world to produce grape-based commodities such as wine, raisins, and grape juice. Historically, its productivity has been endangered by its high susceptibility to biotic and abiotic stresses,...
Discerning genes crucial to antimicrobial resistance (AMR) mechanisms is becoming more and more important to accurately and swiftly identify AMR pathogenic strains. Pangenome-wide association studies (e.g. Scoary) identified numerous putative AMR genes.
D The pan-genome tree based on the binary presence/absence matrix of each gene families. The strains were clustered into three major groups (marked as green, blue and purple, respectively) and three singletons (marked as black) W ang et al. BMC Genomics (2024) 25:...