Skip to main content

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

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

Dataset Alignment method MinimalMatchingProbability
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
  1. 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