Gen2Epi: an automated whole-genome sequencing pipeline for linking full genomes to antimicrobial susceptibility and molecular epidemiological data in Neisseria gonorrhoeae

Table 1 Evaluation of the genome assemblies. Measures are median values

	WHO reference strains	Saskatchewan (NML Samples)†	New Zealand	EuroGASP 2013^¥
# samples	11	27	398	1048
Scaffolds	1	1	1	1
Longest Length	2,167,463	2,210,644	2,212,822	2,212,219
Reference Length	2,172,826	2,232,367	2,232,025	2,153,922
GC (%)	52.64	52.49	52.53	52.52
Misassemblies	0	23	11	11
Unaligned Length	91,387	131,041	153,005	223,989
Genome Fraction (%)	95.95	93.88	92.33	92.62
Duplication ratio	1.01	1.01	1.01	1.01
N’s per 100 kb	4195.81	3873.08	5676.20	5874.67
Indels per 100 kb	1.78	30.72	25.14	30.73
Total aligned length	2,085,686	2,080,404	2,050,100	1,988,450
N50^α	2,167,463	2,210,644	2,212,822	2,212,219
NA50^α	2,050,950	225,330	301,699	239,517
NG50^α	2,167,463	2,210,644	2,212,822	2,212,219
NGA50^α	2,050,950	223,320	293,413	240,269

†In one Saskatchewan sample (32657), a large number of reads were filtered out during the trimming process. This most likely is the reason for the poorer values in this case
^¥Six samples were excluded from the analysis due to the lack of SRA numbers
^αN50 is defined as the length of the shortest contig at 50% of the total assembly length. NG50 is similar to N50, except that they are based on genome size rather than assembly size. NA50 and NGA50 are similar to N50 and NG50 except it is based on the alignment of the contigs against a reference genome

ISSN: 1471-2164