Paul Gordon: On the motion of planets, and nanopore signal consensus
Lightning talk: Paul Gordon, MCS, PhD, of the Centre for Health Genomics and Informatics, University of Calgary, described the use of Dynamic Time Warping Barycenter Averaging (DBA), an algorithm used in aligning two sequences to each other, on direct RNA squiggles generated in nanopore sequencing. Using the squiggles generated by yeast enolase, Oxford Nanopore’s RNA sequencing spike-in, he demonstrated several methods of generating alignments: symmetric vs asymmetric, batch vs incremental. He notes that whilst the symmetric batch method is currently considered computationally infeasible, an asymmetric incremental approach has become possible just recently. Paul evaluated the use of three implementations of DBA, which each produced different results – he highlighted that one algorithm, SSG, produced results which were longer than the signal due to spurious events; and explained that a custom voting system can be used to remove these. This approach can be used to align nanopore squiggles to each other in the absence of a model, enabling identification of modified bases without the need to generate a training dataset.