If genome sequences were assembled from PacBio reads and then polished with quiver/arrow iteratively, do I steel need to polish the genome sequences further with Illumina reads?
I've been trying to assemble a few dozen actinobacterial genomes. I have both PacBio and Illumina data and sequencing depths are >100X for both data for all genomes.
I performed hybrid assembly using Unicycler and SPAdes and long-read assembly using Canu and Flye, for all genomes. Then, I compared the assembly results. I found that long-read assemblies were more contiguous than hybrid assemblies for many genomes. So, I chose long-read assemblies and then polished the assemblies by Arrow algorithm of PacBio GenomicConsensus package (https://github.com/PacificBiosciences/GenomicConsensus). I could get stable(?) genome sequences after 1-3 rounds of Arrow polishing. In other words, Arrow didn't correct anything after 1-3 rounds.
But, when I performed polishing of these stable(?) genomes with Illumina reads by using Pilon, Pilon introduced many changes, sometimes including insertion/deletion of >50-100 bp.
Should I believe the Pilon results in these cases? Or, am I doing unnecessary Pilon polishing?