2013

  • [DOI] E. Siragusa, D. Weese, and K. Reinert, “Scalable string similarity search/join with approximate seeds and multiple backtracking,” in Edbt ’13: proceedings of the joint edbt/icdt 2013 workshops, New York, New York, USA, 2013, pp. 370-374.
    [Bibtex]
    @inproceedings{Siragusa:2013dx,
    author = {Siragusa, Enrico and Weese, David and Reinert, Knut},
    title = {{Scalable string similarity search/join with approximate seeds and multiple backtracking}},
    booktitle = {EDBT '13: Proceedings of the Joint EDBT/ICDT 2013 Workshops},
    year = {2013},
    pages = {370--374},
    publisher = {~ACM Request Permissions},
    address = {New York, New York, USA},
    month = mar,
    doi = {10.1145/2457317.2457386},
    isbn = {9781450315999},
    read = {Yes},
    rating = {0},
    date-added = {2014-04-05T07:22:02GMT},
    date-modified = {2016-01-21T08:51:13GMT},
    abstract = {We present in this paper scalable algorithms for optimal string similarity search and join. Our methods are variations of those applied in Masai [15], our recently published tool for mapping high-throughput DNA sequencing data with unpreceded},
    url = {http://dl.acm.org/citation.cfm?doid=2457317.2457386},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Files/EC/EC14F5DB-5321-44F8-BD50-ACC9917030B7.pdf},
    file = {{EC14F5DB-5321-44F8-BD50-ACC9917030B7.pdf:/Users/reinert/Dropbox/Library.papers3/Files/EC/EC14F5DB-5321-44F8-BD50-ACC9917030B7.pdf:application/pdf;EC14F5DB-5321-44F8-BD50-ACC9917030B7.pdf:/Users/reinert/Dropbox/Library.papers3/Files/EC/EC14F5DB-5321-44F8-BD50-ACC9917030B7.pdf:application/pdf}},
    uri = {url{papers3://publication/doi/10.1145/2457317.2457386}}
    }
  • [DOI] E. Siragusa, D. Weese, and K. Reinert, “Fast and accurate read mapping with approximate seeds and multiple backtracking.,” Nucleic acids research, vol. 41, iss. 7, p. e78–e78, 2013.
    [Bibtex]
    @article{Siragusa:2013ir,
    author = {Siragusa, Enrico and Weese, David and Reinert, Knut},
    title = {{Fast and accurate read mapping with approximate seeds and multiple backtracking.}},
    journal = {Nucleic Acids Research},
    year = {2013},
    volume = {41},
    number = {7},
    pages = {e78--e78},
    month = jan,
    publisher = {Oxford University Press},
    affiliation = {Department of Mathematics and Computer Science, Freie Universit{"a}t Berlin, Takustr. 9, 14195 Berlin, Germany and Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany.},
    keywords = {read mapping},
    doi = {10.1093/nar/gkt005},
    pmid = {23358824},
    pmcid = {PMC3627565},
    language = {English},
    read = {Yes},
    rating = {5},
    date-added = {2013-02-01T08:24:19GMT},
    date-modified = {2016-01-14T20:09:32GMT},
    abstract = {We present Masai, a read mapper representing the state-of-the-art in terms of speed and accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2-4 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a method for multiple backtracking. Approximate seeds, compared with exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds by taking advantage of the repetitiveness of next-generation sequencing data. Combined together, these two methods significantly speed up approximate search on genomic data sets. Masai is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and binaries for Linux, Mac OS X and Windows can be freely downloaded from http://www.seqan.de/projects/masai.},
    url = {http://nar.oxfordjournals.org/content/41/7/e78.full},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Articles/2013/Siragusa/Nucleic%20Acids%20Res%202013%20Siragusa.pdf},
    file = {{Nucleic Acids Res 2013 Siragusa.pdf:/Users/reinert/Dropbox/Library.papers3/Articles/2013/Siragusa/Nucleic Acids Res 2013 Siragusa.pdf:application/pdf;Nucleic Acids Res 2013 Siragusa.pdf:/Users/reinert/Dropbox/Library.papers3/Articles/2013/Siragusa/Nucleic Acids Res 2013 Siragusa.pdf:application/pdf}},
    uri = {url{papers3://publication/livfe/id/115946}}
    }
2016-02-16T11:02:25+00:00