Table 2.
Time performance of pairwise alignment algorithms
| 100 |
1K |
10K |
100K |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HiSeq | ONT | d = 1% | d = 5% | d = 20% | d = 1% | d = 5% | d = 20% | d = 1% | d = 5% | d = 20% | d = 1% | d = 5% | d = 20% | ||
| Gap-affine (Exact) | WFA | 0.06 | 2.46 | 0.09 | 0.37 | 1.55 | 0.14 | 0.93 | 6.93 | 0.43 | 7.28 | 66.00 | 8.49 | 102.00 | 2542.00 |
| KSW2-Z2 | 2.42 | 15.23 | 2.41 | 2.79 | 3.06 | 16.43 | 16.47 | 16.64 | 188.40 | 188.40 | 189.00 | 2146.00 | 2136.00 | 2139.00 | |
| SeqAn | 18.18 | 180.60 | 18.28 | 19.17 | 22.64 | 184.80 | 190.80 | 213.60 | n/a | n/a | n/a | n/a | n/a | n/a | |
| ParaStrip | 77.40 | 530.40 | 77.40 | 75.60 | 70.80 | 603.60 | 602.40 | 572.40 | n/a | n/a | n/a | n/a | n/a | n/a | |
| ParaScan | 12.03 | 69.00 | 11.85 | 11.89 | 11.99 | 75.00 | 75.00 | 75.00 | 746.40 | 747.00 | 747.00 | n/a | n/a | n/a | |
| ParaDiag | 17.80 | 130.20 | 17.53 | 17.58 | 17.66 | 141.60 | 141.60 | 141.60 | n/a | n/a | n/a | n/a | n/a | n/a | |
| Gap-affine (Banded) | WFA-Adap | 0.07 | 1.51 | 0.09 | 0.50 | 2.20 | 0.16 | 0.68 | 2.75 | 0.17 | 0.68 | 3.00 | 0.26 | 1.53 | 6.97 |
| Gaba | 1.26 | error | 1.28 | 1.33 | error | 0.68 | 0.74 | error | 0.60 | 0.81 | error | 0.72 | 0.76 | error | |
| ParaBand | 3.71 | 8.26 | 3.75 | 3.89 | 4.17 | 4.04 | 4.51 | 5.34 | 4.87 | 6.39 | 8.87 | 8.11 | 11.81 | 20.43 | |
| Others | Edlib | 1.75 | 2.28 | 1.73 | 1.82 | 1.94 | 1.95 | 2.03 | 2.73 | 3.67 | 4.50 | 7.39 | 6.95 | 19.34 | error |
| BitPAl | 0.47 | 2.18 | 0.47 | 0.47 | 0.47 | 2.27 | 2.31 | 2.33 | 21.44 | 21.44 | 21.47 | 212.40 | 212.40 | 212.40 | |
| KSW2-D2 | 2.87 | 18.13 | 2.86 | 3.23 | 3.49 | 19.56 | 19.64 | 19.81 | 219.60 | 219.60 | 220.20 | 2385.00 | 2380.00 | 2452.00 | |
Note: Running time in seconds obtained by the different pairwise alignment algorithms on real and simulated datasets. Penalties used for all tests correspond to the ones used by BWA-MEM. Alignment algorithms have been grouped in three categories: ‘Gap-affine (Exact)’ for exact algorithms that use gap-affine penalties, ‘Gap-affine (Banded)’ for approximate algorithms that use gap-affine penalties, and ‘Others’ for exact algorithms that use other distance models (i.e. edit distance or linear-gap penalties). On simulated datasets, results are broken down by error rate. Experiments whose running time exceeded 2 hours are marked as ‘n/a’. Likewise, runs that consistently failed are labelled with ‘error’. Note that WFA-Adapt was executed using WFmin = 10 and WFdiff = 50.