Extended Data Fig. 2: Illustration of basecaller-guided DTW.

(a) Generating of ref-moves from raw basecaller moves and a minimap2 alignment. The minmap2 ‘CIGAR’ corresponding to the basecalled read alignment is ‘9M1I6M1D3M’. K-mers coordinates are defined relative to the central base, which is defined for each pore model based on its substitution matrix (Fig. 2a). (b) A standard NxM DTW matrix, where N = M = 5. Cells are colored by their Manhattan distance from (1,1), which corresponds to the band which they will be contained in. The red line represents the ref-moves which will guide band placement. (c) The same DTW matrix overlaid with bands centered on the ref-moves (band width W = 3). (d) The DTW band matrix with each row offset by its location in the NxM matrix, which is shaded in the background and rotated 45o. White cells indicate out-of-bounds coordinates. Band start coordinates are indicated by the colored numbers to the left. (e) The DTW band matrix, represented as a standard two-dimensional array. Note that the start coordinates are required to reconstruct the original matrix structure.