I have a small haploid genome (85 Mb) that was assembled with Canu based on ~100x of PacBio Sequel reads. In addition, a batch of 40 Gbp Hi-C Illumina reads was sequenced to perform scaffolding. The assembly has been polished with Arrow, but there is not a third dataset of Illumina reads to polish with Pilon. I was wondering if I could instead use the Hi-C reads to perform the Illumina polishing step by mapping one or both ends of the reads individually to the assembly. However, given the nature of Hi-C reads, I am a little concerned that the uneven coverage and chimeric reads could have a negative impact. Anyone has previous experience with this approach? Is it a good idea to use Hi-C reads to polish an assembly?