combine different hybrid assembly

Question

[mariachiaracascarano]

Hi everybody, I have builted six hybrid assemblies of the same bacterial genome (nanopore and miseq data assembled with flye or canu and polished with pilo)n. unfortunately completeness (busco) is approxilmately 79% for each one of them.

I am hoping that the missing part are differnt in differen assemblies and I would like to find a tool that aligns them and generate a consensus to recover eventual missing parts..

Any opinion/suggestion?? Thanks a lot, Chiara

[lieven.sterck]

suggestion: before embarking on the merging assembly route, why not first evaluate if indeed the missing parts are different? If not you will be doing a long quest (and potentially lots of work) to end up with no or only marginal improvement.

I believe Flye can do this though (using the sub-assemblies option)

[mariachiaracascarano]

Well, that was indeed part of my concern, thanks a lot for your comment.