Table 1.

Benchmark results comparing HPG Aligner to BWA MEM and Bowtie 2

RL	MR (%)	HPG Aligner		BWA MEM		Bowtie 2
		CM	Time	CM	Time	CM	Time
100	0.1	98.77	20.57	96.99	29.34	94.67	29.40
	1	98.22	19.66	96.65	33.34	92.98	29.15
	2	97.45	17.46	96.11	37.62	90.52	29.04
150	0.1	99.54	22.90	98.09	43.35	96.71	47.61
	1	99.29	22.09	97.96	49.12	95.93	46.50
	2	98.96	18.13	97.72	54.03	94.73	46.36
400	0.1	99.93	31.35	99.12	124.16	98.82	209.26
	1	99.78	30.49	99.06	142.81	98.71	221.92
	2	99.58	26.30	98.95	157.65	98.56	200.11
800	0.1	99.95	35.57	99.42	279.54	99.29	4604.90
	1	99.74	35.00	99.38	312.55	99.24	2750.26
	2	99.47	34.70	99.28	340.46	99.18	2894.38

Notes: Percentages of correct mapping (CM) and runtimes in min (Time) are displayed for different read length in base pairs (RL) and percentages of mutation rate [MR(%)]. For RLs, >800 bp Bowtie2 was unable to finish in 3 days.