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 👍

[mobinasri]

Hi @MariBGO Sorry for the late response. As long as you have an assembled sequence and you know the expected coverage along your desired regions you should be able to run Flagger. Though one problem might be that if the number of observations is low (for example the total length of the region is smaller than 5Mb) Flagger might not be able to fit parameters confidently.