Table 1 Scores of algorithms when aligning short reads to REF-1
From: Mora: abundance aware metagenomic read re-assignment for disentangling similar strains
Algorithm | Strain | Species | Genus | ||||||
|---|---|---|---|---|---|---|---|---|---|
F1 | Sensitivity | Precision | F1 | Sensitivity | Precision | F1 | Sensitivity | Precision | |
Pufferfish | 62.12 | 47.27 | 90.58 | 66.04 | 50.25 | 96.29 | 67.92 | 51.68 | 99.05 |
Mora + Pufferfish | 66.20 | 50.37 | 96.53 | 67.04 | 51.01 | 97.75 | 68.49 | 52.11 | 99.87 |
AugPatho2 + Pufferfish | 66.62 | 50.69 | 97.14 | 66.90 | 50.90 | 97.55 | 68.49 | 52.11 | 99.87 |
Bowtie2 | 84.54 | 78.04 | 92.20 | 88.94 | 82.11 | 97.01 | 91.21 | 84.21 | 99.48 |
Mora + Bowtie2 | 87.59 | 80.86 | 95.54 | 89.22 | 82.37 | 97.32 | 91.48 | 84.46 | 99.79 |
AugPatho2 + Bowtie2 | 89.03 | 82.19 | 97.10 | 89.64 | 82.76 | 97.77 | 91.50 | 84.47 | 99.80 |
Kraken2 | NA | NA | NA | 88.19 | 83.57 | 93.36 | 92.36 | 87.52 | 97.77 |
Clark | 59.38 | 55.21 | 64.23 | 91.12 | 84.71 | 98.57 | 92.04 | 85.58 | 99.57 |