Flagger with sequencing with target enrichment?

[MariBGO]

Hi, I love the concept of your tool, and am wondering if it would be appropriate to use in a more special l case. I want to evaluate haplotype-resolved de-novo assemblies of a complex region, and I have both HiFi and ultra-long ONT reads. Am I right in thinking if the HiFi reads are obtained with capture probes, flagger would not work due to uneven coverage distribution? And on that note, would you foresee that target enrichment (adaptive sampling) with ONT would work with flagger on the enriched ROI assembly?

Thanks 👍