What I am missing in the whole review so far, is at least a brief section about meta data / annotation in pangenome graphs. If you want to build precise graphs, you need to make sure that people are able to understand and interpret them, right? Please correct me here!
Building them alone without any meta information will do something for you like comparing populations on a structural level. But especially in human, we want to take a look at annotated regions.
As far as I know, only vg is able to integrate annotation from a GFF file?
Are there any other options?
How can we annotate non reference-based graphs?
Is a liftover of annotations possible or desired in the future?
But I am really not sure, if there should be a section about such a topic in a Precision pangenomics paper. Open for discussion.
subwaystation
commented
4 years ago
What I am missing in the whole review so far, is at least a brief section about meta data / annotation in pangenome graphs. If you want to build precise graphs, you need to make sure that people are able to understand and interpret them, right? Please correct me here! Building them alone without any meta information will do something for you like comparing populations on a structural level. But especially in human, we want to take a look at annotated regions.
But I am really not sure, if there should be a section about such a topic in a
Precision pangenomicspaper. Open for discussion.