Table 4 Time consumption of six tools. SURPI was running in the “comprehensive mode”
From: MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data
Dataset | Pathogens | MegaPath | SURPI | Centrifuge | CLARK | Kraken | Kraken2 |
|---|---|---|---|---|---|---|---|
1 | Enterovirus D | 48 min | 4 h 34 min | 4 min | 18 min | 3 min | 12 min |
2 | Human immunodeficiency virus | 12 min | 3 h 29 min | 1 min | 8 min | 1 min | 7 min |
3 | Enterovirus D | 4 h 55 min | 14 h 57 min | 9 min | 22 min | 28 min | 13 min |
4 | Hepatitis C virus | 1 h 45 min | 5 h 13 min | 3 min | 10 min | 12 min | 6 min |
5 | Hepatitis C virus | 1 h 18 min | 4 h 6 min | 3 min | 14 min | 10 min | 9 min |
6 | Human immunodeficiency virus | 26 min | 3 h 51 min | 1 min | 7 min | 1 min | 12 min |
7 | Human immunodeficiency virus | 11 min | 3 h 22 min | 1 min | 8 min | 1 min | 15 min |
8 | Hepatitis B virus | 58 min | 5 h 9 min | 7 min | 12 min | 9 min | 28 min |
9 | Hepatitis B virus | 1 h 4 min | 4 h 20 min | 4 min | 13 min | 9 min | 1 h 11 min |