Table 4.

Expected results from scaffolding the C. elegans Flye assembly using ntLink with gap-filling based on the steps documented in Basic Protocol 2. Using the gap-filling feature of ntLink in addition to scaffolding increased the Contig NG50 and NGA50 lengths to be equivalent with their “Scaffold” statistic counterparts. Furthermore, while the intermediate ntLink scaffolds file prior to gap-filling had a sharp increase in the number of N’s per 100 kbp (14.4 compared to 0.0 in the baseline), the gap-filling step sealed the majority of the gaps (14.4 vs. 0.02 N’s per 100 kbp before and after gap-filling, respectively).

Assembly	Number of sequences >= 3 kbp	Scaffold NG50 length (Mbp)	Contig NG50 length (Mbp)	Scaffold NGA50 length (Mbp)	Contig NGA50 length (Mbp)	Number of misassemblies	# N’s per 100 kbp
Flye baseline	63	3.6	3.6	2.3	2.3	75	0.00
Flye + ntLink (before gap-filling)	33	6.8	4.0	3.7	2.5	66	14.36
Flye + ntLink	33	6.8	6.8	3.9	3.9	64	0.02
Flye + ntLink + Racon	33	6.9	6.9	3.0	3.0	58	0.01