Table 2 Benchmarking results of the pathogen detection tools on a mock metagenomic dataset
From: MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data
Dataset | Spiked bacteria | Similarity to reference | MegaPath | SURPI | Centrifuge | CLARK | Kraken | Kraken2 |
|---|---|---|---|---|---|---|---|---|
rank (# read) | ||||||||
1 | Enterococcus hirae | 20.6% | 13 (579) | 96 (123) | 18 (7.3 K) | 386 (74) | 65 (315) | 83 (207) |
2 | Corynebacterium halotolerans | 29.6% | 14 (526) | n/a (0) | 241 (331) | 457 (58) | 80 (205) | 77 (220) |
3 | Clostridium botulinum | 38.3% | 8 (1.7 K) | 62 (260) | 65 (1.5 K) | 108 (465) | 65 (304) | 37 (625) |
4 | Corynebacterium falsenii | 42.1% | 9 (1.2 K) | n/a (0) | 208 (403) | n/a (0) | 85 (192) | 61 (328) |
5 | Gardnerella vaginalis | 56.2% | 6 (20.2 K) | 23 (7.3 K) | 14 (9.7 K) | 17 (4.9 K) | 13 (4.7 K) | 14 (6.6 K) |
6 | Pasteurella multocida | 60.4% | 6 (19.8 K) | 25 (2.9 K) | 21 (6.2 K) | 23 (2.8 K) | 14 (3.6 K) | 14 (5.6 K) |
7 | Micrococcus luteus | 73.7% | 4 (25.5 K) | 14 (24.7 K) | 10 (17.2 K) | 13 (12.6 K) | 11 (16.6 K) | 11 (16.9 K) |
8 | Gallibacterium anatis | 75.8% | 4 (37.4 K) | 11 (34 K) | 10 (17.8 K) | 12 (18.3 K) | 11 (17.7 K) | 11 (18 K) |
9 | Citrobacter freundii | 77.6% | 4 (38.5 K) | 14 (21.4 K) | 8 (27.2 K) | 13 (10.4 K) | 11 (18.6 K) | 12 (18.6 K) |
10 | Haemophilus parainfluenzae | 85.8% | 4 (38.7 K) | n/a (0) | 10 (18.0 K) | 12 (20.2 K) | 11 (17.4 K) | 11 (18.8 K) |
11 | Leuconostoc gasicomitatum | 91.6% | 4 (39.0 K) | 10 (38.4 K) | 9 (21.8 K) | 11 (22.6 K) | 11 (21.4 K) | 11 (21.5 K) |
12 | Human campylobacteriosis | 95.6% | 4 (34.6 K) | 13 (28.1 K) | 8 (30.6 K) | 12 (19.0 K) | 11 (19.2 K) | 11 (18.4 K) |