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

BMC Bioinformatics

Table 7 Genome completeness improvement after filling gaps using OMACC and nanoGapFiller on 12 species

Species	Scaffold N50 (nt)
Species	Before gap filling	Filling using OMACC	Filling using nanoGapFiller
A. vari	64,556	78,980	7,589,442
B. japonicum	143,477	290,961	1,830,875
B. pseudomallei	86,778	99,967	113,112
C. hutchinsonii	129,478	212,390	1,935,216
E. carotovora	71,290	100,730	680,365
E. coli	78,648	140,985	1,222,147
N. farcinica	176,628	846,096	5,627,295
P. putida	127,879	127,879	4,873,348
P. syringae	79,967	90,066	366,420
S. agal	71,533	1,399,536	2,406,989
S. coelicolor	108,454	120,270	213,619
S. ynec	175,767	300,280	1,774,968

Here, the gaps are identified using simulated optical maps and alignment method SOMA2

ISSN: 1471-2105