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Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

Figure 2

Two alignments of assemblies to the finished sequence of BAC GQQD.

The original Atlas assembly created two scaffolds only covering 73.2% of the finished sequence. Note the misplaced 20 Kb segment in the Atlas assembly. The UMD+Atlas assembly of GQQD correctly places the 20 Kb section originally misplaced and creates a single scaffold of the BAC covering 93.3% of the finished sequence. This UMD+Atlas assembly used reliable overlaps. This was the BAC that gave Atlas the most trouble.

Figure 2

doi: https://doi.org/10.1371/journal.pone.0001836.g002