Tags: #pangenome #pggb #wfmash #seqwish #smoothxg #vg #gwas
[! info] Purpose Construct and analyze the North American Vitis super-pangenome
This GitHub repository is associated with the following article: Cochetel N, Minio A, Guarracino A, Garcia JF, Figueroa-Balderas R, Massonnet M, Kasuga T, Londo JP, Garrison E, Gaut BS, Cantu D (2023) A super-pangenome of the North American wild grape species. Genome Biology 24: 290 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03133-2.
- Generate the alignments with wfmash
- Construct the pangenome with seqwish
- Polish the pangenome with smoothxg
- Model the gene pangenome
- Graph-inferred gene pangenome
- Infer variants from the graph
- Annotate variants
- Variant genotyping
- Pan-GWAS
MIT License