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

Table 4 Results for real datasets

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

ISSN: 1748-7188