ILP-based maximum likelihood genome scaffolding

BMC Bioinformatics

Table 2 Runtime (in seconds) for scaffolding single-genome datasets.

genome	bundle	SILP1	SILP2	OPERA	MIP
staph	1	1237	6.4	2538.1	35.8
	2	738	4.5	1456.5	17
	3	305	4	878.5	12.834
	5	142	3.9	386.9	10.54
	7	51	4.3	241	10.115
rhodo	1	1134	10	2297	118.953
	2	632	4.1	455.2	25.3
	3	486	3.6	5.7	10.995
	5	86	3.4	2	8.778
	7	75	3	1.6	8.217
chr14	1	-	64.7	-	706.3
	2	-	27.6	99.25	189.685
	3	629	25.5	11	137.67
	5	370	21.5	12	107.85
	7	400	19.25	10.75	94.9875
NA12878 2x	1	-	55.2	-	89.3
	2	-	1670	76.49	53.28
	3	37751	3878	7875	121.61
	5	27341	3183	4270	134.6
	7	27470	3626	2180	125.66

All timing was captured only during the scaffolding phase of each tool, all read alignment and formatting procedures were excluded from timing. The number is the average of 10 runs for each genome. A dash (-) indicated the tool was unable to complete in the allotted time of 2 days for staph,rhodo,chr14 and 3 days for NA12878.

ISSN: 1471-2105