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