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Table 6 Summary of performance. Comparison of the performance of the tools on each of the datasets. When multiple samples were tested, the number of samples appears in parentheses, and average performance is reported. For the parallel samples results are for the evaluation of the metagenome based on the plasmidome, and precision and recall are plasmidome read-based. Unless otherwise stated, F1 score is used. Note that in the simulations, SCAPP mpSpades

From: SCAPP: an algorithm for improved plasmid assembly in metagenomes

Test

Ranking

Simulations (7)

SCAPP > Recycler > mpSpades

Human gut metagenomes (20)

SCAPP mpSpades > Recycler

Plasmidome

SCAPP > Recycler mpSpades

Parallel: within tool

mpSpades > SCAPP Recycler

Parallel: “overall”, across tools

SCAPP > Recycler > mpSpades

Parallel: precision

SCAPP ≈ mpSpades Recycler

P arallel: recall

Recycler > mpSpades ≈ SCAPP