Fig. 1

Nanopore basecalling maps signal to sequence. a To basecall a single read, the time series of current signal is fed into a neural network basecaller which outputs for each measurement the probabilities of each base plus a blank gap character. This probability profile is then decoded to find the most likely basecalled sequence. b To constrain our pair decoding algorithm, each read was basecalled individually and the alignment of the resulting sequences was used to define a region in signal space that banded our 2D beam search