misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads

BMC Bioinformatics

Table 1 Performance on assembly of E.coli simulated reads data

	#scf	N50 (kbp)	#scf_cor	N50_cor (kbp)	#Misass (TP,FP,FN)^a	Precision	TPR	#Corr.^b	Time (min)	Memory (GB)
misFinder	71	172.8	74	172.8	27 / 0 / 1	1.0	0.964	8	2	0.8
QUAST	71	172.8	-^c	151.2	27 / 9 / 1	0.75	0.964	-	1	0.4
REAPR	71	172.8	74	172.8	13 / 0 / 15	1.0	0.464	-	17	0.4

^aNumber of Assembly errors were called by misFinder, QUAST and REAPR, including TP (true positives) and FP (false positives), while FN (false negatives) is the number of assembly errors that were not called
^bNumber of correct assemblies corresponding to structural variations called by misFinder
^cQUAST did not output the number of broken scaffolds
The bold data reflected the best values for each column

ISSN: 1471-2105