Table 3 Results for simulated paired-end reads
From: HIA: a genome mapper using hybrid index-based sequence alignment
Aligner | Time | % Aligned | % Unique [% Err] | % Q10 [% Err] |
|---|---|---|---|---|
(a) Illumina-like 100Â bp reads (paired) | ||||
 HIA | 1009 | 99.96 | 97.17 [0.0859] | 96.75 [0.0510] |
 BWA | 2554 | 99.79 | 97.70 [0.0954] | 97.49 [0.0692] |
 BWA MEM | 646 | 99.99 | 98.03 [0.0282] | 97.95 [0.0172] |
 Bowtie2 | 1691 | 97.13 | 97.09 [1.2711] | 93.73 [0.0128] |
 SOAP2 | 586 | 84.54 | 82.75 [0.3356] |  |
 SeqAlto | 2945 | 99.61 | 97.15 [0.0833] | 97.02 [0.0788] |
(b) Illumina-like 150Â bp reads (paired) | ||||
 HIA | 1153 | 99.99 | 98.10 [0.0780] | 97.89 [0.0537] |
 BWA | 5380 | 99.78 | 98.17 [0.0983] | 98.06 [0.0876] |
 BWA MEM | 649 | 99.99 | 98.43 [0.0137] | 98.39 [0.0083] |
 Bowtie2 | 2348 | 97.13 | 97.12 [0.9904] | 94.14 [0.0083] |
 SOAP2 | 856 | 75.25 | 74.04 [0.3487] |  |
 SeqAlto | 7191 | 99.58 | 97.80 [0.0723] | 97.74 [0.0698] |