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

BMC Bioinformatics

Table 5 Running time (in seconds) of nanoGapFiller at different settings of pruning threshold MinimalMatchingProbability

Dataset	Alignment method	MinimalMatchingProbability
Dataset	Alignment method	0 (no pruning)	\(10^{-8}\)	\(10^{-5}\) (default)	\(10^{-2}\)
Simulated optical maps	SOMA2	2123	90	88	53
Real optical maps	SOMA2	46	13	11	13
Real optical maps	refAligner	5953	1620	1227	941

Here, the gaps are identified using both simulated and real optical maps of E. coli species. CPU: AMD Opteron 6344; OS: Ubuntu 16.04; Python version: 3.6.7

ISSN: 1471-2105