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For the last twenty years fragment assembly in DNA sequencing followed the “overlap - layout - consensus” paradigm that is used in all currently available assembly tools. Although this approach proved to be useful in assembling clones, it faces difficulties in genomic shotgun assembly: the existing algorithms make assembly errors and are often unable to resolve repeats even in prokaryotic genomes. Biologists are well-aware of these errors and are forced to carry additional experiments to verify the assembled contigs.
Pevzner et al. (Sun,) studied this question.
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