Hybrid Assembly approaches and advantage of having a circular genome assembly

Question

[SergeW]

Hi all,

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.

Kind regards,

Serge

[rthapa]

Hi, were you able to find the answer?