Table 3.

Performance of de novo assemblies before and after the bridging step of NECAT.

Species	Stats	Contig	Assembly size (Mb)	Max (Kb)	NG50 (Kb)	MA/local MA	NGA50 (Kb)	QV
E. coli	Before	1	4.6	4587	4587	2/10	3977	17.7
	After	1	4.6	4595	4595	2/3	3984	18.5
S. cerevisiae	Before	20	12.3	1530	816	28/29	596	22.3
	After	19	12.3	1529	937	26/35	708	23.1
A. thaliana	Before	150	122.9	14,556	11,150	800/1284	535	15.7
	After	136	122.9	14,567	11,157	886/1304	582	16.0
D. melanogaster	Before	320	143.0	14,923	9612	1120/1424	4930	19.4
	After	277	142.8	21,505	18,072	1117/1333	6323	20.2
C. reinhardtii	Before	64	113.3	8997	5515	838/2345	706	19.3
	After	54	113.4	9014	6169	831/2273	732	19.8
O. sativa	Before	154	372.2	22,009	9241	466/7765	3206	15.5
	After	120	373.1	22,094	9650	479/4873	3311	16.0
S. pennellii	Before	1604	991.9	22,857	3704	5762/13,324	927	15.1
	After	1344	991.8	22,879	4802	5813/12,592	992	15.2
NA12878 (rel3,4)	Before	2151	2791.6	50,857	11,980	811/6716	8334	16.0
	After	1494	2798.4	73,248	14,066	964/4591	9538	16.6
NA12878 (rel6)	Before	1604	2848.6	95,968	18,488	809/1514	12,079	22.6
	After	1047	2846.9	95,975	20,913	948/1467	13,441	23.1

“Contig” is the total number of contigs in assembly. “Assembly size” is the total number of base pairs in assembly. “Max” is the length of the largest contig. “NG50” indicates that 50% of reference genome size was contained in contigs having length ≥ n. “NGA50” is NG50 of aligned blocks that contigs are broken into at mis-assembly breakpoints. “MA/local MA” are the numbers of misassemblies and local misassemblies evaluated using QUAST. “QV” is defined as $10\times {\log }_{10}\left(\frac{\mathrm{100kbp}}{\#\mathrm{mismatches}\mathrm{per}\mathrm{100}\mathrm{kbp}+\#\mathrm{indels}\mathrm{per}\mathrm{100}\mathrm{kbp}}\right)$, where “# mismatches per 100 kbp” and “# indels per 100 kbp” are evaluated by QUAST.