Table 3. Accuracy and running time on R9 data.

The results of base calling were aligned to the reference using BWA-MEM [28]. The first column reports the percentage of reads that aligned to the reference on at least 90% of their length. The accuracy was computed as the number of matches in the alignment divided by the length of the alignment. The speed is measured in events per second.

	Aligned reads	Accuracy	Speed
Nanonet	83.2%	83.2%	2057 ev/s
DeepNano (100 hidden units)	81.1%	81.0%	4716 ev/s
DeepNano (50 hidden units)	79.3%	78.5%	7142 ev/s