TABLE 3

Sensitivity and selectivity statistics for assigned taxonomies at genus level, Bokulich_2a

SoftwareNo. of OTUs (no singletons)PRF1No. of taxonomies
TPFNFP
TotalChimericKnownOther
De novo
    usearch521,5220.3410.51803551317
    Swarm7,0840.3210.48180387229
    uclust20,0840.2510.41805341534
    usearch6122,9870.2410.391805641834
    sumaclust9,5750.2410.381805741538
Closed reference
    usearch525710.3710.541803031314
    sortmerna3960.3610.53180314261
    uclust1,0530.3610.53180326260
    usearch611,0270.3610.53180324280
Open reference
    uclust10,1690.2510.41805241929
    usearch619,4140.2510.41805341831
    sortmerna_sumaclust9,2720.2410.391805551634
  • a P, precision; R, recall; F1, F measure, TP, true positive; FN, false negative; FP, false positive. The last three columns represent a refined breakdown of FP data, including false-positive taxonomies for which all comprising OTUs were classified as chimeric (using UCHIME) (chimeric), mapped to BLAST’s NT database with ≥97% similarity (known), or mapped to BLAST’s NT database with <97% similarity (other).