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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 100 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 150 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]
  1. Time measurement is elapsed time (second). Unique refers to MAPQ ≥ 1 if MAPQ available. Q10 refers to MAPQ ≥ 10