Table 2.
Results for simulated single-end reads
| Aligner | Time | % Aligned | % Unique [% Err] | % Q10 [% Err] |
|---|---|---|---|---|
| (a) Illumina-like 100 bp reads (unpaired) | ||||
| HIA | 464 | 100.00 | 96.57 [0.4314] | 95.80 [0.2151] |
| BWA | 1242 | 98.11 | 94.73 [0.1711] | 94.60 [0.1562] |
| BWA MEM | 265 | 100.00 | 96.30 [0.0497] | 95.27 [0.0153] |
| Bowtie2 | 1291 | 99.95 | 99.63 [2.4252] | 94.22 [0.0208] |
| SOAP2 | 264 | 79.37 | 76.27 [0.4679] | |
| SeqAlto | 1459 | 99.69 | 96.33 [0.2861] | 96.04 [0.2156] |
| (b) Illumina-like 150 bp reads (unpaired) | ||||
| HIA | 530 | 100.00 | 97.56 [0.2552] | 97.26 [0.1643] |
| BWA | 2464 | 98.00 | 95.55 [0.0953] | 95.48 [0.0866] |
| BWA MEM | 355 | 100.00 | 97.36 [0.0210] | 96.41 [0.0053] |
| Bowtie2 | 2069 | 99.97 | 99.87 [1.6663] | 95.99 [0.0094] |
| SOAP2 | 525 | 68.72 | 66.78 [0.2806] | |
| SeqAlto | 3608 | 99.68 | 97.25 [0.1947] | 97.10 [0.1490] |
| (c) 454-like 250 bp reads (unpaired) | ||||
| HIA | 1009 | 99.96 | 98.28 [0.4189] | 94.38 [0.1772] |
| BWA-SW | 3157 | 99.86 | 97.61 [0.6735] | 94.38 [0.0357] |
| BWA MEM | 1497 | 100.00 | 97.92 [0.0767] | 97.26 [0.0346] |
| Bowtie2 | 2947 | 99.59 | 83.40 [0.5980] | 36.44 [0.0011] |
| (d) 454-like 400 bp reads (unpaired) | ||||
| HIA | 1378 | 99.76 | 98.48 [0.1557] | 96.17 [0.0397] |
| BWA-SW | 5144 | 100.00 | 95.89 [0.2084] | 94.00 [0.0284] |
| BWA MEM | 2426 | 99.99 | 98.46 [0.0471] | 97.98 [0.0238] |
| Bowtie2 | 6597 | 99.96 | 88.35 [0.3048] | 32.93 [0.0000] |
Time measurement is elapsed time (second). Unique refers to MAPQ ≥ 1 if MAPQ available. Q10 refers to MAPQ ≥ 10