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Table 4 Results for real datasets

From: HIA: a genome mapper using hybrid index-based sequence alignment

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
  1. Time measurement is elapsed time (second). Unique refers to MAPQ ≥ 1 if MAPQ available. Q10 refers to MAPQ ≥ 10