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Table 1 Alignment accuracy (upper panel) and speed (lower panel) of HmmUFOtu and three other aligners benchmarked with four simulated datasets

From: HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies

Program

Random

V4

V1 V3

V3 V5

 

Alignment accuracy (%)

hmmufotu

96.57

100.00

98.11

100.00

hmmalign

73.45

99.66

100.00

100.00

nhmmer

91.50

100.00

98.12

100.00

blastn

100.00

100.00

100.00

100.00

 

Speed (reads ∙ s− 1 ∙ cpu−1)

hmmufotu

77.1

155.1

86.8

56.2

hmmalign

24.2

38.2

26.8

21.0

nhmmer

44.6

77.5

47.6

41.4

blastn

0.228

0.228

0.222

0.220

  1. A correct alignment is defined as the aligned consensus locus overlapping with at least 90% of the true locus. Speed is measured as reads per second per processor. All HMM aligners used their own trained HMM models from the GreenGenes 97_OTUS reference sequence alignment; NCBI blastn used the best alignment among all hits. Accuracy results are based on the aggregate of 20 replicate samples; speed results are based on the average of 20 samples