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

Table 2 Results for simulated single-end reads

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]

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

ISSN: 1748-7188