Table 2.
Comparing SPUMONI and minimap2 across various metrics on simulated ZymoMC reads of varying levels of accuracy
| Accuracy, throughput, and index size on simulated mock community reads at various level of accuracy | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Read accuracy (%): |
85 |
90 |
||||||||||
| Reference: |
One genome ref |
Pan-genome ref |
One genome ref |
Pan-genome ref |
||||||||
| Reference size: |
56 MB |
56 MB |
28 MB |
31 GB |
31 GB |
16 GB |
56 MB |
56 MB |
28 MB |
31 GB |
31 GB |
16 GB |
| Approach: | SPUMONI-ms | SPUMONI | minimap2 | SPUMONI-ms | SPUMONI | minimap2 | SPUMONI-ms | SPUMONI | minimap2 | SPUMONI-ms | SPUMONI | minimap2 |
| Accuracy | 56.21 | 83.35 | 87.53 | 70.08 | 95.43 | 99.16 | 78.28 | 88.32 | 90.76 | 94.48 | 99.50 | 99.50 |
| Precision | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
| Recall | 54.89 | 82.85 | 87.15 | 69.18 | 95.29 | 99.13 | 87.15 | 87.97 | 90.48 | 94.32 | 99.49 | 99.49 |
| Specificity | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
| F1-score | 70.88 | 90.62 | 93.13 | 81.78 | 97.59 | 99.56 | 93.13 | 93.13 | 95.00 | 97.08 | 99.74 | 99.74 |
| Peak RSS (GB) | 0.63 | 0.08 | 0.17 | 6.24 | 1.90 | 8.07 | 0.63 | 0.08 | 0.17 | 6.24 | 1.90 | 8.07 |
| Index size (GB)a | 0.68 | 0.09 | 0.10 | 6.20 | 1.90 | 31.00 | 0.68 | 0.09 | 0.10 | 6.20 | 1.90 | 31.00 |
| Throughput (bp/s) | 134,690 | 614,665 | 398,415 | 28,731 | 111,813 | 6,441 | 177,572 | 709,018 | 409,104 | 33,829 | 125,914 | 6,617 |
| Read accuracy (%): |
95 |
99 |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Reference: |
One genome ref |
Pan-genome ref |
One genome ref |
Pan-genome ref |
||||||||
| Reference size: |
56 MB |
56 MB |
28 MB |
31 GB |
31 GB |
16 GB |
56 MB |
56 MB |
28 MB |
31 GB |
31 GB |
16 GB |
| Approach: | SPUMONI-ms | SPUMONI | minimap2 | SPUMONI-ms | SPUMONI | minimap2 | SPUMONI-ms | SPUMONI | minimap2 | SPUMONI-ms | SPUMONI | minimap2 |
| Accuracy | 86.48 | 91.00 | 90.86 | 99.60 | 99.65 | 99.40 | 89.76 | 92.20 | 91.30 | 99.65 | 99.60 | 99.50 |
| Precision | 100.00 | 99.94 | 100.00 | 100.00 | 99.95 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 99.95 | 100.00 |
| Recall | 86.07 | 90.78 | 90.58 | 99.59 | 99.69 | 99.39 | 89.45 | 91.96 | 91.04 | 99.64 | 99.64 | 99.49 |
| Specificity | 100.00 | 98.31 | 100.00 | 100.00 | 98.31 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 98.31 | 100.00 |
| F1-score | 92.52 | 95.14 | 95.06 | 99.80 | 99.82 | 99.69 | 94.43 | 95.81 | 95.31 | 99.82 | 99.80 | 99.74 |
| Peak RSS (GB) | 0.63 | 0.08 | 0.17 | 6.24 | 1.90 | 8.07 | 0.63 | 0.08 | 0.17 | 6.24 | 1.90 | 8.07 |
| Index size (GB)a | 0.68 | 0.09 | 0.10 | 6.20 | 1.90 | 31.00 | 0.68 | 0.09 | 0.10 | 6.20 | 1.90 | 31.00 |
| Throughput (bp/s) | 209,163 | 790,409 | 425,320 | 37,130 | 135,463 | 6,672 | 235,712 | 928,459 | 479,523 | 38,556 | 129,574 | 6,259 |
a
The reported index size for SPUMONI-ms and SPUMONI includes only the positive index and not the null index because the null index can be used offline and deleted before the analysis.