FGAP: an automated gap closing tool

BMC Research Notes

Table 3 Software comparison in E. coli assembly

	Original assembly	FGAP	FGAP + Long*	GapCloser	GapFiller	IMAGE
Nº of gaps	123	26	2	22	25	19
Nº contigs (≥ 1000 bp)	116	80	73	82	85	87
Local misassemblies	2	9	2	12	12	21
Complete + partial genes	4325 + 44	4377 + 34	4388 + 27	4375 + 35	4367 + 35	4389 + 67
N50	66462	132608	172148	112396	132608	110934
Inserted bases (bp)	-	3133	6931	6140	3098	37217
Execution time	-	42 s	2 m 55 s	1 m 19 s	19 m 23 s	2 h 46 m 29 s

The evaluation was performed by QUAST script v2.3 [16] (all metrics are in Additional file 1). The gene number was calculated based on a reference list with 4497 genes. *FGAP + Long stands for PacBio’s long reads used directly as datasets.

ISSN: 1756-0500