Table 5 Time (T, in seconds) and recall (R, as a percentage of exact alignments) for aligners across different datasets on a single node
From: Fast noisy long read alignment with multi-level parallelism
Dataset | Size | Metric | Minimap2 | Parasail | ParaHAT | WFA | WFA-GPU |
|---|---|---|---|---|---|---|---|
(SSE) | (SSE) | (SSE+GPU) | (CPU) | (GPU) | |||
E. coli | 628 | T (s) | 69.37 | 110.43 | 46.70 | 3.10 | 2.45 |
R (%) | 100 | 100 | 100 | 99.99 | 99.68 | ||
S. cer. | 1569 | T (s) | 153.17 | 269.51 | 105.71 | 6.44 | 5.37 |
R (%) | 100 | 99.93 | 100 | 100 | 99.29 | ||
D. mel. (sim) | 10M | T (s) | 795.21 | 1401.00 | 609.03 | 40.03 | 35.18 |
R (%) | 100 | 99.99 | 100 | 99.89 | 97.97 | ||
A. tha. | 10M | T (s) | 823.94 | 1453.55 | 541.95 | 45.62 | 39.27 |
R (%) | 100 | 99.99 | 100 | 100 | 99.07 | ||
H. sap. (sim) | 10M | T (s) | 795.17 | 1170.88 | 530.22 | 41.90 | 37.60 |
R (%) | 100 | 99.99 | 100 | 99.97 | 98.60 | ||
H. sap. (real) | 10M | T (s) | 647.86 | 1158.48 | 477.44 | 23.13 | 20.87 |
R (%) | 100 | 99.99 | 100 | 99.89 | 98.49 | ||
D. mel. (real) | 10M | T (s) | 767.07 | 1201.44 | 496.32 | 40.71 | 35.86 |
R (%) | 100 | 99.99 | 100 | 99.99 | 97.99 | ||
PacBio CLR | 10M | T (s) | 1604.32 | 3031.9 | 820.56 | 29.98 | 25.25 |
R (%) | 100 | 99.99 | 100 | 99.82 | 96.51 | ||
PacBio HiFi | 10M | T (s) | 2027.06 | 3822.86 | 1287.12 | 54.39 | 47.27 |
R (%) | 100 | 99.99 | 100 | 99.98 | 98.53 | ||
ONT | 10M | T (s) | 3323.89 | n/a | 2108.81 | 66.69 | 45.64 |
R (%) | 100 | n/a | 100 | 99.99 | 97.63 |