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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