Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph

BMC Bioinformatics

Table 1 Filling the gaps identified using simulated optical maps of E. coli genome

Gap	Reference sequence		OMACC				nanoGapFiller
Gap	#contigs	#bases	#contigs	#bases	CPS	NSS (%)	#contigs	#bases	CPS	NSS (%)
252228–252408r	4	11	4	11	4	100	4	11	4	100
252424r–252466	4	12	46	3316	4	0.72	4	12	4	100
252292–252268r	5	645	5	645	5	100	5	645	5	100
252410r–252292	5	10,858	5	10,858	5	100	5	10,858	5	100
252208–252300	5	199	7	367	5	70.32	5	199	5	100
252538r–252526	6	1256	–	–	–	–	6	1256	6	100
252216r–252238	7	226	31	1546	7	25.51	7	226	7	100
252238–252228	7	1259	7	1259	7	100	7	1259	7	100
251622r–252244	9	30,034	17	30,482	9	99.26	9	30,034	9	100
252244–252386r	10	10,424	10	10,424	10	100	10	10,424	10	100
251936r–252510	14	18,913	–	–	–	–	14	18,913	12	99.86
252408r–252538r	14	20,922	14	20,922	14	100	14	20,922	14	100
252268r–252316	15	3339	19	3701	15	94.86	15	3339	15	100
252300–252312	15	5127	–	–	–	–	15	5127	11	98.93
252132–252226	18	7171	–	–	–	–	18	7171	18	100
252180–252410r	23	22,821	–	–	–	–	24	22,821	20	99.40
252316–252290	23	79,025	–	–	–	–	23	79,025	22	99.99
252312–252424r	24	5431	–	–	–	–	25	5431	23	99.96
252466–252252	25	13,442	–	–	–	–	26	13,442	21	99.97
252226–252216r	42	156,131	–	–	–	–	43	156,131	33	99.93
252486–252208	47	83,834	–	–	–	–	47	83,834	41	99.92
252148–252180	56	50,774	–	–	–	–	59	50,774	44	99.20
252252–252310r	59	118,754	–	–	–	–	60	118,754	53	100

ISSN: 1471-2105