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Table 2 Results for simulated single-end reads

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

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