I have PacBio long reads and Illumina short reads and am trying to identify/learn the best method for hybrid assembly. Currently I have identified either using MaSuRCA pipeline or doing the following:
PacBio based assemblies with Canus (should I correct the pacbio reads first?)
Polish the Canu assemblies with Illumina reads using Pilon
So my question is what is the best approach and if the use of just Canu and Pilon enough?
Any help would be greatly apriciated :)