Circlator: automated circularization of genome assemblies using long sequencing reads

Table 1 Summary of results on 14 bacterial genome assemblies

Species	Ref	HGAP	Circularizable contigs^a,b			Correctly circularized^a			Errors^c
NCTC ID	contigs	contigs	BLAST	Circlator	Minimus2	BLAST	Circlator	Minimus2	BLAST	Circlator	Minimus2
Bacillus subtilis	1	19	1	1	1	1	1	1	5	1	2
NCTC3610			(0,1)	(0,1)	(0,1)	(0,1)	(0,1)	(0,1)
Clostridium difficile	2	11	0	0	0	0	0	0	0	0	0
NCTC13307			(0,0)	(0,0)	(0,0)	(0,0)	(0,0)	(0,0)
Staphylococcus epidermidis	7	9	8	8	8	7	8	4	0	0	4
NCTC13360			(1,7)	(1,7)	(1,7)	(1,6)	(1,7)	(1,3)
Enterobacter cloacae	3	8	1	2	2	1	1	1	0	0	0
NCTC10005			(0,1)	(1,1)	(1,1)	(0,1)	(0,1)	(0,1)
Salmonella Typhimurium	2	7	1	1	2	1	1	1	2	0	1
NCTC13348			(0,1)	(0,1)	(1,1)	(0,1)	(0,1)	(0,1)
Yersinia enterocolitica	2	4	1	1	1	1	1	1	0	0	0
NCTC10963			(1,0)	(1,0)	(1,0)	(1,0)	(1,0)	(1,0)
Staphylococcus aureus	1	3	2	2	2	2	2	1	0	0	0
NCTC10833			(1,1)	(1,1)	(1,1)	(1,1)	(1,1)	(0,1)
Staphylococcus aureus	3	2	1	1	1	0	1	0	0	0	0
NCTC13626			(1,0)	(1,0)	(1,0)	(0,0)	(1,0)	(0,0)
Salmonella Enteritidis	2	2	2	2	2	2	2	1	0	0	0
NCTC13349			(1,1)	(1,1)	(1,1)	(1,1)	(1,1)	(0,1)
Legionella pneumophila	1	2	1	1	1	0	1	0	0	0	0
NCTC11192			(1,0)	(1,0)	(1,0)	(0,0)	(1,0)	(0,0)
Staphylococcus aureus	1	1	1	1	1	1	1	0	0	0	0
NCTC13616			(1,0)	(1,0)	(1,0)	(1,0)	(1,0)	(0,0)
Staphylococcus aureus	1	1	1	1	1	1	1	0	0	0	0
NCTC13277			(1,0)	(1,0)	(1,0)	(1,0)	(1,0)	(0,0)
Bordetella pertussis	1	1	1	1	1	1	1	0	0	0	0
NCTC13251			(1,0)	(1,0)	(1,0)	(1,0)	(1,0)	(0,0)
Salmonella bongori	1	1	1	1	1	0	1	0	0	0	0
NCTC12419			(1,0)	(1,0)	(1,0)	(0,0)	(1,0)	(0,0)
Total	28	71	22	23	24	18	22	10	7	1	7

^aThe first and second numbers in parentheses are counts of contigs corresponding to chromosomes and plasmids, respectively
^bA contig is defined as circularizable if it includes the entire sequence of a chromosome or plasmid, irrespective of the presence or size of an overlap between its start and end
^cAll errors except for those on sample NCTC13360 were false circularizations, where a tool attempted to circularize a contig that should not be circular. All four errors made on sample NCTC13360 were incorrect circularizations, where an attempt was made to circularize a circular contig, but the output contained errors

ISSN: 1474-760X