The quality of the linear reference genome used for constructing a pan-genome

Question

[chiyong4783]

Hello, everyone. Does constructing a pan-genome graph using MC require a haplotype-resolution genome(Like in human pan-genome studies), or can a chromosome-level genome also be used? What are the quality requirements for the linear reference genome used in constructing the pan-genome?

Answer 1

[colindaven]

No, you can use any genome or contig set, it does not have to be haplotype resolved. I would advise you to use chromosome level genome assemblies though as contigs tend to contain redundant material.

However, the reference assembly needs to be chromosome scale. See https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md

[chiyong4783]

Thank you very much for your help.