Table 3:

Basecalling rate in base pairs per second

Basecaller	CPU rate (1 core)	CPU rate (8 cores)	GPU rate
Albacore v1.1.2	2,975	23,800	NA
BasecRAWller	81	648	NA
Chiron	21	168	1,652
Chiron-BS	17	136	1,204

The single-core CPU rate is calculated by dividing the number of nucleotides basecalled by the total CPU time for the basecalling analysis. An 8 core CPU rate is estimated by multiplying single-core CPU rate by 8, based on observed 100% utility of CPU processors in multithreaded mode on 8 cores. The GPU rate was calculated on a Nvidia K80 GPU. The reported rate is the average across all samples analyzed. The GPU rate is not reported for Albacore or BasecRAWller as they have not been developed for use on a GPU. Chiron is also capable of running on a GPU, and its rate in this mode is included in parentheses. Albacore is not capable of running in GPU mode. Albacore v2 was found to have similar performance as Albacore v1.1.2.