How to add a supplementary polishing iteration about flye HOT 3 CLOSED

Hi,
Thank you for your interest!
The reported alignment error rate is for the alignment of raw reads on the current assembly. Even if the assembly is polished, you would expect 12-16% errors coming from the reads, so the numbers you have do not necessarily mean that the genome requires more polishing.

Still, you can make an extra iteration and check if the statistics improve (most likely, for a tiny bit): use '--iterations 3' and '--resume' options to add one polishing iteration to the existing assembly.

from flye.

Hi,

I used the newest version of Flye (2.7-b1585) to handle nanopore reads (~60X, with default parameters except --asm-coverage 30). The assembly (N50: 14.7Mb) is much better than the one produced by Canu. Its Busco reaches almost 90%. The genome can annotate all of hox genes(39 genes) using homology-based prediction. But there are a lot of frameshift mutations in 38 genes.

How to know how many iterations I need to polish? how about the Busco score?

I also check if it's necessary to do more polishes with Racon. However, racon makes the quality of genome assembly worse. Busco score decreases to 86% and more hox genes get 'lost'.

Any suggestions are welcome.

Thanks a lot.

from flye.

Polishing methods are now rapidly developing - it is hard to give a concrete advice on the best strategy. I'd suggest to look into recent literature - this might be a good start: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y

from flye.