Should I do further scaffolding or gap-filling after hybrid assembly with DBG2OLC?
Hi everyone! I have just finished a hybrid assembly on a plant genome using 40x PE Illumina data and 10x PacBio reads (10-20 kb). After hybrid assembly and polishing with DBG2OLC and blasr, I got 3645 backbones (is it the same as scaffolds?) with an N50 of 294 Kb. I was wondering how to further improve this assembly. Should I do further scaffolding or gap-filling? What tools do you suggest for that? Should I mask for repeats? Thanks a lot for your help!
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