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Table 1 Summary of results on 14 bacterial genome assemblies

From: Circlator: automated circularization of genome assemblies using long sequencing reads

Species Ref HGAP Circularizable contigsa,b Correctly circularizeda Errorsc
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
  1. aThe first and second numbers in parentheses are counts of contigs corresponding to chromosomes and plasmids, respectively
  2. 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
  3. 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