• [DOI] K. Reinert, B. Langmead, D. Weese, and D. J. Evers, “Alignment of Next-Generation Sequencing Reads.,” Annual review of genomics and human genetics, vol. 16, pp. 133-151, 2015.
    [Bibtex]
    @article{Reinert:2015ds,
    author = {Reinert, Knut and Langmead, Ben and Weese, David and Evers, Dirk J},
    title = {{Alignment of Next-Generation Sequencing Reads.}},
    journal = {Annual review of genomics and human genetics},
    year = {2015},
    volume = {16},
    pages = {133--151},
    month = aug,
    affiliation = {Department of Mathematics and Computer Science, Freie Universit{"a}t Berlin, 14195 Berlin, Germany; email: knut.reinert@fu-berlin.de , david.weese@fu-berlin.de.},
    doi = {10.1146/annurev-genom-090413-025358},
    pmid = {25939052},
    language = {English},
    read = {Yes},
    rating = {0},
    date-added = {2015-09-08T22:46:25GMT},
    date-modified = {2015-11-26T15:38:48GMT},
    abstract = {High-throughput DNA sequencing has considerably changed the possibilities for conducting biomedical research by measuring billions of short DNA or RNA fragments. A central computational problem, and for many applications a first step, consists of determining where the fragments came from in the original genome. In this article, we review the main techniques for generating the fragments, the main applications, and the main algorithmic ideas for computing a solution to the read alignment problem. In addition, we describe pitfalls and difficulties connected to determining the correct positions of reads.},
    url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=25939052&retmode=ref&cmd=prlinks},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Files/75/7559E08C-FEF5-4C6C-8B06-256C0CF662A7},
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    uri = {url{papers3://publication/doi/10.1146/annurev-genom-090413-025358}}
    }
  • [DOI] M. Holtgrewe, L. Kuchenbecker, and K. Reinert, “Methods for the detection and assembly of novel sequence in high-throughput sequencing data.,” Bioinformatics (oxford, england), vol. 31, iss. 12, pp. 1904-1912, 2015.
    [Bibtex]
    @article{Holtgrewe:2015bna,
    author = {Holtgrewe, Manuel and Kuchenbecker, Leon and Reinert, Knut},
    title = {{Methods for the detection and assembly of novel sequence in high-throughput sequencing data.}},
    journal = {Bioinformatics (Oxford, England)},
    year = {2015},
    volume = {31},
    number = {12},
    pages = {1904--1912},
    month = jun,
    publisher = {Oxford University Press},
    affiliation = {Department of Computer Science, Freie Universit{"a}t Berlin and Max Planck Institute for Molecular Genetics, Berlin, Germany.},
    doi = {10.1093/bioinformatics/btv051},
    pmid = {25649620},
    language = {English},
    read = {Yes},
    rating = {0},
    date-added = {2015-11-11T13:51:39GMT},
    date-modified = {2016-02-10T10:55:48GMT},
    abstract = {MOTIVATION:Large insertions of novel sequence are an important type of structural variants. Previous studies used traditional de novo assemblers for assembling non-mapping high-throughput sequencing (HTS) or capillary reads and then tried to anchor them in the reference using paired read information.
    RESULTS:We present approaches for detecting insertion breakpoints and targeted assembly of large insertions from HTS paired data: BASIL and ANISE. On near identity repeats that are hard for assemblers, ANISE employs a repeat resolution step. This results in far better reconstructions than obtained by the compared methods. On simulated data, we found our insert assembler to be competitive with the de novo assemblers ABYSS and SGA while yielding already anchored inserted sequence as opposed to unanchored contigs as from ABYSS/SGA. On real-world data, we detected novel sequence in a human individual and thoroughly validated the assembled sequence. ANISE was found to be superior to the competing tool MindTheGap on both simulated and real-world data.
    AVAILABILITY AND IMPLEMENTATION:ANISE and BASIL are available for download at http://www.seqan.de/projects/herbarium under a permissive open source license.},
    url = {http://bioinformatics.oxfordjournals.org/content/31/12/1904.full},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Files/28/28042B27-15F4-4BEC-A9DB-B1D0A22E6000},
    file = {{28042B27-15F4-4BEC-A9DB-B1D0A22E6000:/Users/reinert/Dropbox/Library.papers3/Files/28/28042B27-15F4-4BEC-A9DB-B1D0A22E6000:application/pdf;28042B27-15F4-4BEC-A9DB-B1D0A22E6000:/Users/reinert/Dropbox/Library.papers3/Files/28/28042B27-15F4-4BEC-A9DB-B1D0A22E6000:application/pdf}},
    uri = {url{papers3://publication/doi/10.1093/bioinformatics/btv051}}
    }
  • [DOI] L. Kuchenbecker, M. Nienen, J. Hecht, A. U. Neumann, N. Babel, K. Reinert, and P. N. Robinson, “IMSEQ – a fast and error aware approach to immunogenetic sequence analysis,” Bioinformatics (oxford, england), vol. 31, iss. 18, p. btv309–2971, 2015.
    [Bibtex]
    @article{Kuchenbecker:2015kz,
    author = {Kuchenbecker, Leon and Nienen, Mikalai and Hecht, Jochen and Neumann, Avidan U and Babel, Nina and Reinert, Knut and Robinson, Peter N},
    title = {{IMSEQ - a fast and error aware approach to immunogenetic sequence analysis}},
    journal = {Bioinformatics (Oxford, England)},
    year = {2015},
    volume = {31},
    number = {18},
    pages = {btv309--2971},
    month = may,
    publisher = {Oxford University Press},
    affiliation = {Berlin-Brandenburg Center for Regenerative Therapies, Charit{'e} Universit{"a}tsmedizin, Berlin, Department of Computer Science, Freie Universit{"a}t, Berlin, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel, Marien Hospital Herne, Ruhr University Bochum, Bochum and Institute of Medical Genetics and Human Genetics, Charit{'e} Universit{"a}tsmedizin Berlin, Berlin, Germany Berlin-Brandenburg Center for Regenerative Therapies, Charit{'e} Universit{"a}tsmedizin, Berlin, Department of Computer Science, Freie Universit{"a}t, Berlin, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel, Marien Hospital Herne, Ruhr University Bochum, Bochum and Institute of Medical Genetics and Human Genetics, Charit{'e} Universit{"a}tsmedizin Berlin, Berlin, Germany Berlin-Brandenburg Center for Regenerative Therapies, Charit{'e} Universit{"a}tsmedizin, Berlin, Department of Computer Science, Freie Universit{"a}t, Berlin, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel, Marien Hospital Herne, Ruhr University Bochum, Bochum and Institute of Medical Genetics and Human Genetics, Charit{'e} Universit{"a}tsmedizin Berlin, Berlin, Germany.},
    doi = {10.1093/bioinformatics/btv309},
    pmid = {25987567},
    language = {English},
    read = {Yes},
    rating = {0},
    date-added = {2015-09-10T13:08:52GMT},
    date-modified = {2016-01-05T21:09:17GMT},
    abstract = {Abstract Motivation: Recombined T and B cell receptor repertoires are increasingly being studied using next generation sequencing (NGS) in order to interrogate the repertoire composition as well as changes in the distribution of receptor clones under different ...
    },
    url = {http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/bioinformatics/btv309},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Files/6A/6A37250E-2353-4A74-B15E-9B2E1287153F},
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    uri = {url{papers3://publication/doi/10.1093/bioinformatics/btv309}}
    }