An Eulerian path approach to DNA fragment assembly

Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9748-53. doi: 10.1073/pnas.171285098.


For the last 20 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 useful in assembling clones, it faces difficulties in genomic shotgun assembly. We abandon the classical "overlap-layout-consensus" approach in favor of a new euler algorithm that, for the first time, resolves the 20-year-old "repeat problem" in fragment assembly. Our main result is the reduction of the fragment assembly to a variation of the classical Eulerian path problem that allows one to generate accurate solutions of large-scale sequencing problems. euler, in contrast to the celera assembler, does not mask such repeats but uses them instead as a powerful fragment assembly tool.

Publication types

  • Comparative Study

MeSH terms

  • Algorithms*
  • Campylobacter jejuni / genetics
  • Contig Mapping / methods*
  • DNA, Bacterial / genetics
  • Genome, Bacterial
  • Lactococcus lactis / genetics
  • Models, Theoretical
  • Neisseria meningitidis / genetics
  • Sequence Alignment / methods
  • Sequence Analysis, DNA / methods*
  • Software


  • DNA, Bacterial