Table 4.
Aligner | Time | % Aligned | % Unique | % Q10 |
---|---|---|---|---|
(a) Illumina 100 bp reads (unpaired) | ||||
HIA | 369 | 97.71 | 91.23 | 86.41 |
BWA | 2877 | 85.87 | 81.82 | 81.68 |
BWA MEM | 272 | 96.86 | 89.32 | 86.85 |
Bowtie2 | 1291 | 94.96 | 92.11 | 83.69 |
SOAP2 | 283 | 87.29 | 82.29 | |
SeqAlto | 1567 | 89.16 | 85.22 | 84.60 |
(b) 454 400 bp reads (unpaired) | ||||
HIA | 964 | 99.05 | 96.90 | 95.92 |
BWA-SW | 6369 | 99.53 | 96.48 | 92.63 |
BWA MEM | 830 | 99.73 | 96.36 | 94.86 |
Bowtie2 | 6597 | 98.37 | 96.96 | 91.02 |
(c) Illumina 100 bp reads (paired) | ||||
HIA | 1111 | 91.53 | 87.48 | 85.25 |
BWA | 2871 | 88.90 | 86.59 | 86.26 |
BWA MEM | 690 | 93.49 | 90.55 | 89.80 |
Bowtie2 | 1646 | 93.13 | 91.60 | 84.93 |
SOAP2 | 725 | 82.18 | 79.56 | |
SeqAlto | 3370 | 92.04 | 87.82 | 87.55 |
Time measurement is elapsed time (second). Unique refers to MAPQ ≥ 1 if MAPQ available. Q10 refers to MAPQ ≥ 10