Table 3.
Summary of training classes used for PACIFIC.
| Class | Total reads | Number of genome assemblies | Number of taxonomic units | Included species/genus groups |
|---|---|---|---|---|
|
Coronaviridae [ssRNA( +)] |
644,483 | 12 | 12 | Alpha, beta, gamma and unclassified coronaviruses |
|
Influenza [ssRNA(−)] |
1,073,237 | 128 | 125 | Influenza A (H1N1, H2N2, H3N2, H5N1, H7N9, H9N2), Influenza B |
|
Metapneumovirus [ssRNA(−)] |
443,974 | 5 | 1 | Metapneumovirus |
|
Rhinovirus [ssRNA(+)] |
1,339,435 | 130 | 107 | Rhinovirus A and A1, B, C (C1, C2, C10), other enterovirus |
|
SARS-CoV-2 [ssRNA(+)] |
865,303 | 87 | 1 | SARS-CoV-2 |
| Human | 3,531,425 | 1a | 1 | Human transcriptome |
| Total | 7,897,857 | 363 | 247 |
aGENCODE canonical transcripts were used to represent human reads in RNA-seq data.