Improving read mapping using additional prefix grams

Kim, Jongik; Li, Chen; Xie, Xiaohui

doi:10.1186/1471-2105-15-42

BMC Bioinformatics

Table 1 Rabema benchmark results of mapping simulated 100k reads of length 100bp against HG18

From: Improving read mapping using additional prefix grams

	Time (min:sec)		Benchmark category																Peak
Mapper	1 thr	16 thrs	All				All-best				Any-best				Recall				memory
Hobbes2	9:43	1:33	99.85	100.0	100.0	100.0	99.99	100.0	100.0	100.0	99.99	100.0	100.0	100.0	98.97	100.0	99.90	99.68	14.6 GB
				99.99	99.94	97.48		100.0	100.0	99.84		100.0	100.0	99.84		99.34	99.04	99.77
Hobbes	19:36	3:35	98.34	99.29	99.28	98.93	98.67	98.86	99.02	99.00	98.99	99.19	99.31	99.34	96.91	98.66	97.99	96.68	20.7 GB
				97.40	93.78	87.84		98.19	92.85	89.21		98.55	93.25	90.14		95.33	91.68	90.17
Masai	18:11	−	99.83	100.0	100.0	100.0	99.94	100.0	100.0	100.0	99.94	100.0	100.0	100.0	99.03	100.0	100.0	100.0	16.9 GB
				99.73	99.18	97.69		99.69	98.73	98.52		99.69	98.73	98.52		99.71	98.77	98.56
RazerS3	60:06	42:07	99.90	100.0	100.0	100.0	99.99	100.0	100.0	100.0	99.99	100.0	100.0	100.0	99.09	100.0	100.0	100.0	4.5 GB
				100.0	99.86	98.44		100.0	100.0	99.92		100.0	100.0	99.92		100.0	100.0	99.92
Bowtie2	−	266:21	99.74	100.0	100.0	100.0	99.97	100.0	100.0	100.0	99.97	100.0	100.0	100.0	98.80	100.0	99.70	99.40	37.7 GB
				100.0	99.55	95.75		100.0	99.70	98.35		100.0	99.72	98.45		99.10	98.70	98.50
BWA	75:04	12:20	97.73	100.0	99.98	99.64	98.89	100.0	99.98	99.61	98.90	100.0	99.98	99.61	97.91	100.0	99.98	99.45	4.8 GB
				93.47	82.91	75.15		93.03	78.87	70.57		93.03	78.98	70.73		92.47	78.55	71.18
GEM	5:19	2:56	97.74	100.0	99.99	99.84	99.86	100.0	99.88	99.81	99.92	100.0	99.96	99.93	98.66	100.0	99.42	99.12	4.3 GB
				97.36	88.78	68.31		99.47	99.28	97.34		99.69	99.61	97.67		98.17	98.29	98.64
Bowtie2*	0:31	0:32	91.34	98.87	97.75	93.55	97.08	97.65	97.33	95.69	99.29	100.0	99.45	97.65	95.96	97.75	96.88	95.00	3.2 GB
				81.07	53.90	21.95		95.38	93.98	93.74		97.41	96.24	95.89		94.60	93.33	93.95
BWA*	2:08	0:25	92.27	100.0	99.82	96.90	98.79	100.0	99.83	99.41	98.83	100.0	99.89	99.49	97.31	100.0	99.17	97.76	4.5 GB
				79.11	45.49	16.99		92.57	78.26	70.34		92.70	78.60	70.73		90.39	77.11	70.35
GEM*	0:31	0:13	94.48	100.0	99.38	97.61	99.86	100.0	99.88	99.81	99.92	100.0	99.95	99.92	98.62	100.0	99.28	99.06	4.3 GB
				90.10	69.11	35.34		99.41	99.17	97.37		99.72	99.61	97.75		98.24	98.35	98.94

all: all mappings within the given edit distance threshold; all-best: all best mappings (i.e., all mappings with lowest edit distances); any-best: any best mappings (i.e., any mapping with lowest edit distances).

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ISSN: 1471-2105

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