Table 2 Performance on simulated metagenome datasets. The number of covered plasmids (# covered) reports the number of the simulation plasmids that were covered by reads along at least 95% of their length. The set of covered plasmids is used as the gold standard in calculating the performance metrics. The numbers in parentheses are the median plasmid lengths (in kbp). F1 score is presented as a percent
From: SCAPP: an algorithm for improved plasmid assembly in metagenomes
Recycler | mpSpades | SCAPP | |||||||
|---|---|---|---|---|---|---|---|---|---|
Sample | # genomes | # plasmids | # covered | # plasmids | F1 | # plasmids | F1 | # plasmids | F1 |
Sim1 | 10 | 9 (5.9) | 9 (5.9) | 7 (5.6) | 50.0 | 1 (4.3) | 20.0 | 5 (5.6) | 57.1 |
Sim2 | 50 | 47 (19.3) | 37 (13.5) | 20 (3.8) | 40.1 | 9 (5.0) | 39.1 | 23 (5.5) | 43.3 |
Sim3 | 200 | 210 (22.4) | 136 (9.6) | 61 (3.6) | 32.8 | 27 (7.0) | 32.3 | 48 (5.8) | 42.9 |
Sim4 | 200 | 177 (25.4) | 132 (12.7) | 62 (4.1) | 40.8 | 29 (6.0) | 36.5 | 51 (6.2) | 48.9 |
Sim5 | 300 | 318 (23.9) | 253 (9.6) | 115 (3.6) | 35.2 | 53 (5.1) | 33.8 | 100 (6.5) | 47.5 |
Sim6 | 400 | 480 (13.5) | 368 (9.1) | 138 (3.0) | 28.5 | 59 (5.5) | 27.1 | 118 (5.5) | 36.5 |
Sim7 | 500 | 571 (17.3) | 410 (8.7) | 132 (3.5) | 31.1 | 69 (5.3) | 28.1 | 141 (5.2) | 40.5 |