The latest CCS technology

Open fengcong3 opened this issue 6 years ago • 1 comments

hi, I saw a preprint article using the latest CCS technology from pacbio.The article is here https://www.biorxiv.org/content/10.1101/519025v2 .Can this tool generate simulation data using the latest error model?If so, how do I set the parameters? thanks

Mar 20 '19 01:03 fengcong3

You could try it with the CCS parameter simply setting the accuracy quite high, but you might need to regenerate the model table because of increased accuracy. Unfortunately the original authors don't have a function to regenerate it, but it looks like it is just a fit exponential.

I would be highly skeptical of simulated results generated without fitting to real data, if you can get some actual data you can then at least validate that the simulated data looks similar in some aspects. In particular I'm not sure if PacBio data has a bias for certain k-mers, but Nanopore has a strong bias, that is not factored into this simulator.

If you manage to get it working if you could post how you got it, and/or what you needed to change I would appreciate it. Thanks!

Mar 20 '19 21:03 pfaucon