simulated sequences with Ns

[zya067025]

Hi PBSIM3,

I would like to use PBSIM3 to generate some simulated ONT sequences for my ~12kb DNA sequences. What I want to do is to assemble these simulated ONT sequences. However, the assembler is not able to take sequences with Ns. I am just wondering how can I use PBSIM3 to generate simulated ONT sequences without Ns? Thanks!

[yukiteruono]

Thank you for your using PBSIM3.
If your reference genome contains N, PBSIM3 will generate reads containing N. However, PBSIM3 does not have an option to remove N, so please remove N from your reference genome yourself before running PBSIM3.