I want to assemble a bacterial genome using canu for the Minion data and correcting it with Illumina reads (I will also try to compare it to a hybrid assembler like SPades) but I do not know which strategy to use. As I understood well there are several ways to proceed : - Assembling with canu and then correcting the errors with a hybrid polish like pilon - Correcting the reads from Minion with Illumina with NaS for example and then assebling the genome
Which method would be the best ? I would prefere the first method because canu is already thought to correct the errors but I am not sure as our coverage from the Illumina data is better.
Thank you very much for your help, Cheers, Sofia