polishing strategy and rounds

[binlu1981]

Hi,

I have an assembly generated using wtdbg2 which could use wtpos-cns performing polishment. Will I get a better result through performing additional long- or short-reads polishing steps using the NextPolish? Would it produces conflict results using different polishing tools? How many rounds can reach best status and how to determine?

[moold]

Yes, see our paper, Hu, Jiang, et al. "NextPolish: a fast and efficient genome polishing tool for long read assembly." Bioinformatics (Oxford, England) (2019)

[binlu1981]

Thanks for quickly reply. Your paper mainly focus on short reads corrections and documented that two rounds is good enough, so I plan to perform one round PacBio long-reads + two round short-reads correction using wtpos-cns, and finally use NextPolish to do two round short-reads correction. Will it work? The assembly is ~2Gb and short-reads are about 100 Gb. My severs has ~330 Gb memory, is it enough to run NextPolish?

[moold]

The memory is enough, NextPolish does not require much memory. I do not test wtpos-cns, for NextPolish, two round short-reads correction is enough, but if you want a more accurate assembly, you can try more iterations.