Figure 5.

Total absolute alignment and base-calling times in readfish for different aligners on PromethION and GridION. Note that the base-called reads are streamed into the aligner for mappy and mappy-rs, so the two processes are occurring in parallel. Each scatter point represents a batch of accumulated signal chunks being analyzed by readfish, and the color represents the mean base-called length of reads in the batch. The ‘break_read_chunk_ms‘ for each device is indicated on the x- and y-axis of each plot as a dashed line, representing the amount of time each chunk of signal data recorded in a batch represents. Ideally, the total batch time should fall below this line. The marginal axes for each facet display Kernel Density estimation plots of the distribution of times for their axis. The PromethION/mappy combination has a different axes scale than the other facets, as batch processing times quickly lagged. When using the Dorado alignments, it was not possible to deconvolute the Alignment time from the base-calling time, as alignments are returned to readfish alongside the base-called signal; therefore, points will fall on x = y.