Comparison of different technologies for the decipherment of the whole genome sequence of Campylobacter jejuni BfR-CA-14430

Table 2 Summary of the assembler performance based on different sequencing technologies

Index	Data	Assembler	#Contigs	#bp total length	#Chromosomal contigs; #bp	#plasmid; #bp	Insertions, deletions and SNPs	Covered by illumina reads	Sequence identity of flaA
A	Illumina	SPAdes	30	1,666,0451	30; 77,674 (N50)^a	Cannot be directly detected	0^b	99.9^c	100
B	PacBio	HGAP	2	1,733,585	1; 1,668,827	1; 64,758	155	99.46	100
C	PacBio	Flye	2	1,687,377	1; 1,645,611	1; 41,766	255	99.99	100
D	PacBio	CLC	2	1,688,161	1; 1,646,367	1; 41,794	253	99.97	100
E	PacBio + Illumina	Unicycler	3	1,684,748	2; 1,631,764/ 11,212	1; 41,772	0	99.9	100
F	PacBio + Illumina	wtdbg2	3	1,693,078	2; 1,644,895/ 6,442	1; 41,741	47	99.65	100
G	MinION	Flye	2	1,720,675	1; 1,678,003	1; 42,673	24,439	99.36	99.6
H	MinION + Illumina	Unicycler	2	1,687,752	1; 1,645,980	1; 41,722	20	99.94	100
I	MinION + Illumina	wtdbg2	5	1,672,121	4; 1,648,160/ 15,620/12,211/6,130	1/41,957	169	98.15	100

^aQuality of draft genomes can be measured by the N50 value
^bIllumina paired-end data is taken as ground truth for identification of SNPs, insertions and deletions
^cAs result of the scaffolding process, performed by the SPAdes assembler, contigs with known distance, but unknown sequence content, are connected by “N”s. Thus, the SPAdes assembly is not covered by Illumina data by 100%

ISSN: 1757-4749