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Table 2 Assessment of different parameters to verify long-read overlaps and their impact on LazyB assembly quality on fruit fly

From: LazyB: fast and cheap genome assembly

Varification parameters Compl.[%] #ctg #MA
Direction 80.13 608 111
Direction + offset 80.08 622 103
Direction + offset + incomplete mapping 80.04 1263 121
No mapping 80.15 801 113
  1. Overlaps are indicated by anchors and evaluated by pairwise long-read alignments. They are considered valid if: the relative direction suggested by the anchor matches that of the pairwise alignment (direction); the offset is sufficiently similar for both methods (offset); at least 75% of the overlap is found as direct alignment (incomplete mapping); the overlap indicated by the anchor is less than or equal to 1 kbp or a pairwise alignment is possible (no mapping). Column descriptions: completeness of the assembly, #ctg: number of contigs, #MA: number of mis-assemblies (breakpoints relative to the reference assembly)