Could we use LRBinner after scaffolding in WGA?

[franztastic]

Hello everyone,

I've used your tool in different metagenomics project and now, as suggested by my supervisor in a WGA, I've used as a decontamination tool after scaffolding.

Following, I've tried doing manual curation with Pretext and it seems that I have no contacts between my scaffolds and 33 different chromosomes.

However, I've tested running LRBinner and, later, YAHS and my results are completely different, having now 17 chromosomes with a lot of contact between my scaffolds but with a super-low coverage.

I see that the tool is not made to be used for decontamination after scaffolding but I'm wondering why results are that different.

Thank you very much for your answer!