Are there any free open source software tools available for simulating Oxford Nanopore reads?
2$\begingroup$ What are you planning on simulating data for? In my opinion, given the wealth of publicly available real datasets, there is little need for simulation except in very specific use cases. $\endgroup$– Scott GiganteMay 22, 2017 at 23:37
4$\begingroup$ It's often useful to simulate a variant or some other type of genomic artifact to evaluate whether a tool or set of tools can correctly identify the artifact. This is much easier to do on simulated data where you know the exact answer, and is extremely valuable even if the simulated data isn't a perfect reflection of real data. $\endgroup$– Daniel StandageMay 23, 2017 at 2:32
Simulators designed specifically for Oxford Nanopore:
General long read simulators:
For an exhaustive list of existing read simulators, see page 15 of my thesis, Novel computational techniques for mapping and classifying Next-Generation Sequencing data.
By chance, just today I've heard of a nanopore read simulator, NanoSim. It is released under a GPL license. I have never used it, though...
In addition to the already mentioned NanoSim, there is also SiLiCO and ReadSim (although it hasn't been updated in over 2 years, so I am not sure how relevant it is at this point considering how fast the technology is progressing).
The best nanopore read simulators would be associated with the best base-callers. For a base-caller to effectively model the DNA strand, it needs to take into account the expected underlying electrical model together with the associated signal noise (both in the time dimension as well as the amplitude dimension). In theory, it should be possible to reverse the algorithm and generate an electrical signal given an underlying sequence.
Unfortunately, I'm not aware of any tools that attempt to simulate nanopore reads at the electrical level. Any "nanopore read simulator" that concentrates only on base sequence would need to encompass all the possible base-calling software models that exist, which is an impossible task (particularly given how quickly ONT updates their own base callers).