search

lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
419 stars 38 forks source link

Graph construction methods #111

Closed tanakash1028 closed 8 months ago

tanakash1028 commented 8 months ago

Thank you for developing the great algorithm. I have a question regarding the method of graph construction and visualization of minigraph.

According to Extended Data Fig. 3 of a Nature paper entitled "A draft human pangenome reference," the copy number polymorphisms of chromosomal segments are represented by bubbles. (attached screenshot)

screenshot2024-03-26 18 34 10

I am wondering whether the number of bubbles increases if there are three or more copy number variations of chromosomal segments. If there were three segments (S2, S3, and "S4") on the attached figure, would we see an additional bubble on minigraph? I mean, would there be two bubble loops? Or would the number of bubbles not increase, and the path will cycle two times through the one bubble?"

lh3 commented 8 months ago

I am wondering whether the number of bubbles increases if there are three or more copy number variations of chromosomal segments.

Yes if they are generally <100kb in length

tanakash1028 commented 7 months ago

@lh3 Thank you very much for your prompt reply.