Polishing genome assembly

Question

[Lissa Cruz Saavedra]

Hi everyone

I am working on genome assembly. I already run an assembly using PacBio hifi reads and hifiasm software. However, I want to improve more my assembly. I am wondering if I can use a Nanopore data and Pilón software for polishing. Could it increase the error rate for my data?.

Thanks for your answer!

Answer 1

[Michael]

If you have Hifi reads your error rate should already be quite good, therefore polishing with potentially longer and slightly more error-prone Nanonopore reads might not do any good. You might rather try to improve contingency. Do you have Hi-C data available? If you already have the Nanopore reads, I would try to use the Nanopore reads for gap-closure and scaffolding. Possibly, generate a hybrid assembly using both technologies to complement each other e.g. with the Flye assembler.