Single molecule sequencing-guided scaffolding and correction of draft assemblies

BMC Genomics

Table 3 Quality comparisons for S. aureus USA300 assemblies using downsampled PacBio long reads

Coverage	Tools	Contigs	N50	NG50	AvgIdentity	Reloc	Trans	Inv	Total T	Stg1 T	Stg2 T
293.63x	SMSC	13	2585902	2585902	99.99	3	0	0	6m51s	2m12s	4m39s
	Canu	5	1492711	1492711	99.98	2	0	0	36m26s	N/A	N/A
	ScaffMatch	14	1099804	1099804	99.98	28	2	0	N/A	N/A	1m7s
	ScaffMatch ^∗	31	611114	479066	99.98	16	0	0	N/A	N/A	2m12s
17.54x	SMSC	55	91135	91135	99.84	8	0	1	2m15s	1m5s	1m10s
	Canu	52	89147	84231	99.64	2	0	0	6m8s	N/A	N/A
	ScaffMatch	13	1131851	1131851	99.85	30	0	1	N/A	N/A	1m6s
	ScaffMatch ^∗	106	50567	49351	99.87	2	0	0	N/A	N/A	25s
23.47x	SMSC	18	641333	641333	99.94	3	0	0	2m37s	56s	1m41s
	Canu	27	224570	224570	99.85	2	0	0	7m29s	N/A	N/A
	ScaffMatch	14	1091191	1091191	99.94	29	0	0	N/A	N/A	54s
	ScaffMatch ^∗	70	89077	89077	99.95	3	0	0	N/A	N/A	32s
29.31x	SMSC	12	2569515	2569515	99.95	6	0	0	3m6s	1m4s	2m2s
	Canu	15	426754	426754	99.92	2	0	0	9m54s	N/A	N/A
	ScaffMatch	13	1091146	1091146	99.96	34	0	0	N/A	N/A	54s
	ScaffMatch ^∗	55	149552	149552	99.97	6	0	0	N/A	N/A	37s

The ScaffMatch* means the ScaffMatch that takes error-corrected PacBio long reads as input

ISSN: 1471-2164