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Fig. 3 | BMC Genomics

Fig. 3

From: Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

Fig. 3

Steps of the stitch.pl algorithm. Consensus genome maps (blue) are shown aligned to in silico maps (green). Alignments are indicated with grey lines. CMAP orientation for in silico maps is indicated with a “+” or “-” for positive or negative orientation respectively. a The in silico maps are used as the reference. b The alignment is inverted and used as input for stitch.pl. c The alignments are filtered based on alignment length (purple) relative to total possible alignment length (black) and confidence. Here assuming all alignments have high confidence scores and the minimum percent aligned is 30 % two alignments fail for aligning over less than 30 % of the potential alignment length for that alignment. d Filtering produces an XMAP of high quality alignments with short (local) alignments removed. e High quality scaffolding alignments are filtered for longest and highest confidence alignment for each in silico map. The third alignment (unshaded) is filtered because the second alignment is the longest alignment for in silico map 2. f Passing alignments are used to super scaffold (captured gaps indicated in dark green). g Stitch is iterated and additional super scaffolding alignments are found using second best scaffolding alignments. h Iteration takes advantage of cases where in silico maps scaffold consensus genome maps as in silico map 2 does. Stitch is run iteratively until all super scaffolding alignments are found

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