Table 2.

Summary of assembler performance

Strain ID	Newbler statistics		AMOScmp statistics		Automatic combined assembly		Manual combined assembly
	Contigs >500 nt, total size	N50a, longest contig	Contigs >500 nt, total size	N50, longest contig	Contigs >500 nt, total size	N50, longest contig	Contigs >500 nt, total size	% gapfill, longest contig
NM13220	175 2.07M	22K 106K	202 2.06M	21K 77K	195 2.25M	31K 107K	57 2.30M	1.8% 398K
NM10699	102 2.10M	52K 143K	116 2.10M	43K 113K	83 2.17M	59K 143K	40 2.18M	1.1% 435K
NM15141	147 2.06M	33K 171K	190 2.05M	22K 115K	139 2.21M	36K 171K	50 2.28M	2.0% 759K
NM9261	99 2.09M	51K 184K	133 2.07M	37K 170K	128 2.16M	64K 231K	27 2.21M	1.6% 866K
NM18575	133 2.09M	30K 172K	147 2.09M	29K 88K	220 2.40M	53K 231K	N/Ac	N/A
NM5178	89 2.13M	56K 136K	107 2.12M	42K 131K	104 2.17M	59K 136K	N/A	N/A
NM15293	92 2.08M	52K 144K	110 2.06M	42K 132K	107 2.10M	59K 144K	N/A	N/A
BBE001	146 5.05M	70K 212K	178 5.04M	61K 173K	214 5.03M	80K 252K	N/A	N/A
BBF579	272 4.84M	57K 88K	321 4.84M	46K 94K	272b 4.84M	57K 88K	N/A	N/A

Data for each strain are presented in rows. Statistics from standalone assemblers (Newbler and AMOScmp) are presented together with results of the combining protocol (default output of the pipeline) and an optional, manually assisted predictive gap closure protocol.

^aN50 is a standard quality metric for genome assemblies that summarizes the length distribution of contigs. It represents the size N such that 50% of the genome is contained in contigs of size N or greater. Greater N50 values indicate higher quality assemblies.

^bNo improvement was detected from the combined assembly in strain BBF579, and the original Newbler assembly was automatically selected.

^cThe manual combined assembly protocol was not performed for these projects.