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.