Tag: PGGB
Open problems in genomics 2023
As a user and developer I am grateful for all the efficient, clever and really helpful tools and pipelines put out there by the community. I’d like to use this page to suggest any open questions from my point of view, i.e gaps in the field where talented developers might…
Explanation of vg deconstruct vcf output
Explanation of vg deconstruct vcf output 0 Hello, I am struggling in understanding the vg deconstruct vcf output. I’m working on a pangenome (17 genomes, reference included) and the file has been created thanks to the pggb pipeline. Is there a detailed explanation of the vcf decomposed file anywhere? Especially…
Creating a variation graph for Giraffe alignment from assemblies
Creating a variation graph for Giraffe alignment from assemblies 0 I have a collection of ~100 4.5 megabase haploid assemblies that I would like to map to using giraffe. However, I am not completely clear on what the best practices are to construct the graph starting from the assemblies. I…
