%0 Journal Article %1 Pevzner:2001aa %A Pevzner, P A %A Tang, H %A Waterman, M S %D 2001 %J Proc Natl Acad Sci USA %K Algorithms, Alignment, Analysis, Bacterial, Campylobacter Contig DNA, Genome, Lactococcus Mapping, Models, Neisseria Sequence Software, Theoretical, jejuni, lactis meningitidis, %N 17 %P 9748--53 %R 10.1073/pnas.171285098 %T An Eulerian path approach to DNA fragment assembly %V 98 %X For the last 20 years, fragment assembly in DNA sequencing followed the överlap-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 överlap-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.

@article{Pevzner:2001aa, abstract = {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.}, added-at = {2007-09-17T20:19:41.000+0200}, affiliation = {Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA.}, author = {Pevzner, P A and Tang, H and Waterman, M S}, biburl = {https://www.bibsonomy.org/bibtex/285853a4fe7db3494508d6631d10f55ca/dzerbino}, doi = {10.1073/pnas.171285098}, interhash = {b11d55cc83ba3b83d5f6d1301c119899}, intrahash = {85853a4fe7db3494508d6631d10f55ca}, issue = {17}, journal = {Proc Natl Acad Sci USA}, keywords = {Algorithms, Alignment, Analysis, Bacterial, Campylobacter Contig DNA, Genome, Lactococcus Mapping, Models, Neisseria Sequence Software, Theoretical, jejuni, lactis meningitidis,}, language = {English}, local-url = {file://localhost/Users/danielzerbino/Documents/Papers/2001/Pevzner/Proc%20Natl%20Acad%20Sci%20USA%202001%20Pevzner.pdf}, month = Aug, number = 17, pages = {9748--53}, pii = {98/17/9748}, pmid = {11504945}, timestamp = {2007-09-17T20:19:41.000+0200}, title = {An Eulerian path approach to DNA fragment assembly}, uri = {papers://055852FE-1648-42FE-91D0-8CA474D2B905/Paper/p15}, volume = 98, year = 2001 }