I'm currently busy trying out different short, long and hybrid (Illumina+Nanopore) assemblers on real and simulated bacterial data (isolates). I've been focusing on Unicycler, HASLR and HybridSPAdes for the hybrid assemblies and Canu, Flye and Unicycler (Miniasm) for the longread-only assemblies.
My first question is; what is the main difference/advantage in using Unicycler vs a longread assembler (ex. Flye) + Pilon polishing approach? It seems like Unicycler is heavily dependent on the short read assembly it performs.
My second question is; what's the advantage of having a circular genome assembly (for example using Circlator) when your assembly is linear but accurate and complete overall (especially the ends).
Thanks in advance! Any tips and advices on assemblies/polishing/pre-processing are welcome.