polishing strategy choice

[binlu1981]

Hi ruanjue,

After obtaining consensus, which following polishing strategy is better?

1. One round wtpos-cns using long reads, then three round wtpos-cons using short reads
2. One round wtpos-cns + one round racon, then one round wtpos-cons + two round netxpolish using short reads
3. one round racon using long reads, then three round netxpolish using short reads

Thanks for any suggestions Bin

[ruanjue]

I am not sure. I suggest to run wtpoa-cns using long reads, then using short reads, and polishing with other tools.

[binlu1981]

Thanks. Do you mean that run one round wtpos-cns using long reads, and then one round wtpos-cons using short reads, and finally run other polish tools using short reads? In short, do long + short read polishment following your tutorial first, then perform short read polishment using other tools. Would it produces conflict results if using different polishing tools for different round? For example, short reads correction baed on one round wtpos-cons + two round netxpolish.

[ruanjue]

In principle, run long reads first, then run short reads. I know little about the order of short reads polishing. Please have a try.