A super-pangenome of the North American wild grape species

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.

Index

• 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

References

References

License

MIT License