Change Log

Runtime speedup of 4.9X compared to v0.2.
Improved yield at empirical Q30 from 141% in v0.2 to 149%, relative to ccs baseline of 100%. This was achieved through improvements to training data including use of new CHM13 T2T assembly (chm13v2.0_noY) and sequencing.
Added a documentation page with yield metrics for 3 SMRT Cells with different read length distributions.
Updated recommendation for ccs settings to skip very low-quality reads, saving runtime.
Model input condenser layer added, saving runtime.
To save significant runtime, added an option to skip running the model on windows that are already likely to be correct with --skip_windows_above a certain predicted quality from CCS, with a default Q45.
Memory profiling with batch option recommendations.
Add support for TensorFlow SavedModel for portability.
Added base quality calibration tuned for v0.3 model, customizable with --dc_calibration option.
The --min-quailty flag default was changed from 20 to 0 in this version. This change was reverted in v0.3.1.

Acknowledgement

Thanks to Armin Töpfer, Aaron Wenger, and William Rowell at PacBio for advice and collaboration.
Thanks to Felipe Llinares for contributing a new alignment training metric.
Thanks to Moshe Wagner for adding a multiprocessing speedup to the preprocessing stage.
Thanks to Joel Shor for model advice and code reviews.