Which Tool is Better for Genome Polishing Using Illumina and Nanopore Reads: Polypolish vs. Pilon and Racon vs. Medaka?

Question

[Umer]

Hello Reader,

I'm working on polishing a fungal genome assembly generated with Nanopore long reads, supplemented by high-coverage (~100x) Illumina short reads. My goal is to Polish the genome assemblies. I’ve already completed the initial genome assemblies using FLYE from Nanopore reads after adapter trimming using porechop.

Specifically, I’d like guidance on the selection of softwares for polishing:

• For Nanopore Long-Read Polishing: Racon or Medaka ?
• For Illumina Short-Read Polishing: Pilon or PolyPolish for polishing ?

Flye genome assembler also has a polishing step where it requires number of iterations, i have selected 3, so do I need to perform Long-read polishing again ?

• if YES: Should i use the raw FastQ files or QC-trimmed FastQ files (result of porechop which i used to generate assemblies) ?

I’d really appreciate any insights.

Thanks in advance for your help!

[Dunois]

If you've already polished via Flye (during the assembly) I doubt it make sense to do long read polishing again after the fact. I'd just do a round of short read polishing and be done with it. It is exceedingly unlikely that one or the other tool will produce drastically better (or worse) results for the polishing step.

Or just do hybrid assembly. Refer https://doi.org/10.1093/bib/bbad337 and https://doi.org/10.26508/lsa.202201744 for some good tools in this regard (and also some relevant information on polishing).