Scaffolding illumina contigs with nanopore reads

Question

[elena.syp]

Hi!! Does anybody have a good suggestion on software that can scaffold illumina contigs using nanopore reads? Thanks!

Elena

[lieven.sterck]

which ones have you considered already or is this a completely open question to get other peoples advise first?

A bit more info on your specific case might help as well, small genome - large genome? little data -lots of data ? such kind of things ...

[colindaven]

If you can, go the other way for better results. Do a pure nanopore assembly if coverage is sufficient, then use RACON and Nanopolish with your illumina reads to increase the base quality.

There are lots of threads here on how to polish effectively. More info is needed too!