Data availability

[alexbw]

Is it possible to provide example data? Or is it inside of the .mat file?

[jts]

This is a good idea. I'll extract a small segment of our draft assembly and corresponding MinION reads from @nickloman's dataset to act as a tutorial. I'll leave this issue open as a reminder to put this together.

[alexbw]

More broadly, for others wishing to develop further embellishments of HMM-based sequence calling, are larger datasets publicly available at all, and if so, under a license which would allow open source research?

[jts]

Yes, the data in our preprint can be used for development. See supplementary table 3 in here:

http://biorxiv.org/content/biorxiv/early/2015/03/11/015552.full.pdf

This table gives accession numbers that can be used to get the data from the EBI or NCBI.

Let me know if you run into difficulty

[jts]

In addition to the public datasets linked above, there is now a single read bundled as part of the testing framework:

https://github.com/jts/nanopolish/tree/master/test/data

Its use is demonstrated here:

https://github.com/jts/nanopolish/blob/master/nanopolish_test.cpp#L69