I am very new to genomics and currently running MaSurca. Just wanted to know if any polishing steps (pilon or racon) are suggested after assembly?
Thank you for assistance in advance.
I assume, you assemble some sort of long reads mixed with n short read libraries. Depending on your coverage, it might not be necessarily, but I would run it in any case at least once to see how much is polished. Any of the two programs is good, I have worked with pilon, so far.
I have paired end, mate-pair and pacbio reads. I will go ahead with pilon polishing then. Thanks.
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