Table 2.

Comparison of NGS-results obtained from the DNA libraries prepped with the manual and automated workflows.

ID	Species	Manual LP				Automated LPa
		Average read depth	No. of contigs	Contig N50 value	CT	Average read depth	No. of contigs	Contig N50 value	CT
1	A. baumannii	65	122	130,855	5739	56	130	120,793	5739
2	S. aureus	53	93	148,765	10,250	69	57	175,655	10,250
3	S. aureus	44	107	87,218	29,549	71	71	236,617	29,549
4	P. aeruginosa	35	127	253,249	3485	37	125	194,842	3485
5	K. pneumoniae	44	124	249,794	9468	44	127	208,058	9468
6	E. faecalis	82	73	252,526	3279	67	84	171,989	3279
7	S. maltophilia	54	62	404,192	NA	54	74	307,186	NA
8	C. difficile	51	191	153,433	6412	47	191	153,389	6412
9	E. cloacae	37 –	145 –	123,665 –	NA –	50 44	57 56	406,176 406,176	NA NA
10	P. aeruginosa	41 –	60 –	457,320 –	3881 –	39 40	69 63	378,423 391,655	3881 3881
11	K. pneumoniae	46 –	101 –	315,903 –	9559 –	35 41	161 98	259,608 335,928	9559 9559
12	E. coli	42 –	281 –	92,775 –	24,800 –	44 37	260 292	106,206 106,221	24,800 24,800
13	S. aureus	46 –	71 –	157,271 –	20,040 –	69 58	53 45	200,036 181,835	20,040 20,040
14	C. difficile	32 –	241 –	65,117 –	6044 –	44 41	127 140	149,052 188,829	6044 6044
15	C. difficile	50 –	533 –	118,000 –	6759 –	46 47	536 412	112,835 97,762	6759 6759
16	S. aureus	50 –	108 –	108,892 –	34,349 –	56 59	68 58	170,114 196,683	34,349 34,349

CT complex type, LP library preparation, NA not available.

^aThe automated LPs were performed in three independent flowbot ONE runs, with sample 1–8 processed in the first run and samples 9–16 processed in the second and third run for reproducibility testing.