Table 4 Wall-clock runtime in hours of different modes of NanoCaller using 16 CPUs on 49× ONT, 35× CCS, and 58× CLR reads of HG002
NanoCaller mode | snps_unphased | snps | Indels | Both |
|---|---|---|---|---|
Description | Only SNP calling by NanoCaller deep convolutional network model | “snps_unphased” mode followed by WhatsHap SNP call phasing | Only indel calling by NanoCaller using phased BAM input | “snps” mode, followed by read phasing by WhatsHap, and “indels” mode |
ONT | 3.8 | 5.0 | 12.6 | 18.4 |
CCS | 2.7 | 3.2 | 7.6 | 11.2 |
CLR | 3.6 | 4.8 | – | – |