Closed esteinig closed 2 years ago
Thank you for your using PBSIM2. PBSIM2 is intended for error-prone long-read simulations, so it cannot handle more than 99% accuracy, such as PacBio HiFi read and ONT kit 12 chemistry. The next version of PBSIM currently under development has implemented a simulation of PacBio HiFi read. For ONT kit 12 chemistry, we are investigating the characteristics for developing a simulation method.
Thanks! Would be amazing to have this finer-scale control over read accuracy as your tool is the fastest one I could find :)
Hey love the tool - I ran into some issues using the ONT HMM models and
--accuracy-mean
which produces the same results for--accuracy-mean 0.99
(Q20) and--accuracy-mean 0.999
(Q30) - which are in both cases the results for Q20. Is it possible to add support for finer-scale floats for this option?Essentially this command is to simulate Kit12 chemistry (~ mean Q20) for R9.4.1 pores, but produces ~20% perfect reads (Q93)
produces the same output as
When I filter reads by average read quality scores > 90, the perfect reads are removed leaving a Q20 highest read quality, which would be inconsistent with
--mean-accuracy 0.99
and default of--max-accuracy 1.0
. I would expect reads in the simulated dataset between Q20 (1% error) and Q93 (0% error) given these configurations