Polish the genome first or Fill the gaps in the genome first for genome assemblies?

Question

[madnessfish]

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!

Answer 1

[lagartija]

Hi, there are actually several ways to do it ! you can first try-out a hybrid assembly by Spades with nanopore and illumina reads then polish the final assembly with your tool. You can also try to first correct your nanopore reads then do the hydrid assembly with spades (careful with the options that are not exactly the same). I would prefer to go this way.

Now, if your nanopore or you illumina coverage is much higher than the other, you should consider a first assembly with these high coverage reads (for example Flye/Abruijn for nanopore or Spades for illumina) followed by gap-filling and polishing.