Hi there! I am new to de novo genome assemblies. I have searched over the community but it seems there are no answers. I am not so sure which action should go first for finishing a genome. Thanks!
I have assembled a nanopore-based genome and polished using Illumina and Nanopore reads. After all, I tried to scaffold the genome with nanopore reads. Now, I wondered I should fill the gaps with nanopore reads and then polish the genome with Illumina reads (as nanopore reads have high error rates). Or I should scaffold and fill the gaps before I polish the genome. Or maybe the order of action doesn't matter much?
Thank you so much!