Table 2.

FPB and GenoProfiler background removal

Method	Ctg	Clones	Qs	Score	Remark
FPB	1	22	2	0.784	Chloroplast
	2	28	16	0.515	Centromere
	3	6	1	0.780	rDNA
GenoProfiler1	1	150	105	0.420	Wrong assembly
GenoProfiler2	1	22	5	0.767	Chloroplast
	2	22	12	0.556	Centromere

Comparison of contigs produced by FPC (tolerance 0.4 bp, cutoff 1e-20) on a set of 1000 clones of the grapevine physical map project (about 0.2× coverage) and processed with FPB and GenoProfiler. Clones were chosen at random from a set of 30,000 clones for which BAC-end sequences were available. Only contigs with at least 3 clones are presented in the table. For GenoProfiler, we used both default parameters and manually optimized parameters, respectively in methods GenoProfiler1 and GenoProfiler2. Qs, represent the so-called "questionable clones" and score is a probabilistic value reflecting the goodness of contigs in FPC. The last column of the table specifies which kind of clones compose the corresponding contig (from an independent inspection on the BAC-end sequences of the set of selected clones). FPC produced wrong or incomplete assemblies with, respectively, default or manually optimized parameters for GenoProfiler.