Table 1 Benchmarking results of the pathogen detection tools on nine real metagenomic datasets
From: MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data
Dataset | Pathogens | Similarity to reference | MegaPath | SURPI | Centrifuge | CLARK | Kraken | Kraken2 |
|---|---|---|---|---|---|---|---|---|
rank (# read) | ||||||||
1 | Enterovirus D | 18.9% | 33 (608) | 264 (76) | 710 (31) | 1.5 K (1) | 384 (6) | 176 (74) |
2 | Human immunodeficiency virus | 19.0% | 15 (3.8 K) | 63 (1.0 K) | 78 (1.3 K) | 69 (444) | 109 (216) | 32 (1.4 K) |
3 | Enterovirus D | 27.9% | 622 (202) | 788 (50) | 2.5 K (14) | 2.6 K (8) | 1.3 K (9) | 1.5 K (17) |
4 | Hepatitis C virus | 36.3% | 2 (12 K) | 2 (7.4 K) | 65 (2.9 K) | 15 (2.5 K) | 3 (2.4 K) | 31 (4.2 K) |
5 | Hepatitis C virus | 38.4% | 2 (568) | 6 (374) | 379 (150) | 152 (182) | 12 (130) | 231 (218) |
6 | Human immunodeficiency virus | 43.9% | 3 (54 K) | 5 (21 K) | 6 (16 K) | 4 (13 K) | 6 (4.5 K) | 2 (18 K) |
7 | Human immunodeficiency virus | 46.1% | 187 (41) | 421 (19) | 859 (18) | 430 (18) | n/a (0) | 496 (19) |
8 | Hepatitis B virus | 69.4% | 2 (43 K) | 2 (33 K) | 18 (19 K) | 4 (20 K) | 3 (19 K) | 7 (20 K) |
9 | Hepatitis B virus | 72.8% | 2 (3.0 K) | 4 (2.4 K) | 191 (1.5 K) | 41 (1.5 K) | 4 (1.1 K) | 94 (1.5 K) |