2012

  • [DOI] D. Weese, M. Holtgrewe, and K. Reinert, “RazerS 3: faster, fully sensitive read mapping.,” Bioinformatics (oxford, england), vol. 28, iss. 20, pp. 2592-2599, 2012.
    [Bibtex]
    @article{Weese:2012byb,
    author = {Weese, David and Holtgrewe, Manuel and Reinert, Knut},
    title = {{RazerS 3: faster, fully sensitive read mapping.}},
    journal = {Bioinformatics (Oxford, England)},
    year = {2012},
    volume = {28},
    number = {20},
    pages = {2592--2599},
    month = oct,
    publisher = {Oxford University Press},
    affiliation = {Department of Mathematics and Computer Science, Freie Universit{"a}t Berlin, Berlin, Germany. david.weese@fu-berlin.de},
    doi = {10.1093/bioinformatics/bts505},
    pmid = {22923295},
    language = {English},
    read = {Yes},
    rating = {0},
    date-added = {2014-06-18T11:28:14GMT},
    date-modified = {2016-01-14T20:10:02GMT},
    abstract = {MOTIVATION:During the past years, next-generation sequencing has become a key technology for many applications in the biomedical sciences. Throughput continues to increase and new protocols provide longer reads than currently available. In almost all applications, read mapping is a first step. Hence, it is crucial to have algorithms and implementations that perform fast, with high sensitivity, and are able to deal with long reads and a large absolute number of insertions and deletions.
    RESULTS:RazerS is a read mapping program with adjustable sensitivity based on counting q-grams. In this work, we propose the successor RazerS 3, which now supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers' bit-vector algorithm for verification, memory-saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular, long reads with many errors. We extensively compare RazerS 3 with other popular read mappers and show that its results are often superior to them in terms of sensitivity while exhibiting practical and often competitive run times. In addition, RazerS 3 works without a pre-computed index.
    AVAILABILITY AND IMPLEMENTATION:Source code and binaries are freely available for download at http://www.seqan.de/projects/razers. RazerS 3 is implemented in C++ and OpenMP under a GPL license using the SeqAn library and supports Linux, Mac OS X and Windows.},
    url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/bts505},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Articles/2012/Weese/Bioinformatics%202012%20Weese-1.pdf},
    file = {{Bioinformatics 2012 Weese-1.pdf:/Users/reinert/Dropbox/Library.papers3/Articles/2012/Weese/Bioinformatics 2012 Weese-1.pdf:application/pdf;Bioinformatics 2012 Weese-1.pdf:/Users/reinert/Dropbox/Library.papers3/Articles/2012/Weese/Bioinformatics 2012 Weese-1.pdf:application/pdf}},
    uri = {url{papers3://publication/doi/10.1093/bioinformatics/bts505}}
    }
  • [DOI] A. Emde, M. H. Schulz, D. Weese, R. Sun, M. Vingron, V. M. Kalscheuer, S. A. Haas, and K. Reinert, “Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS,” Bioinformatics (oxford, england), vol. 28, iss. 5, pp. 619-627, 2012.
    [Bibtex]
    @article{Emde:2012ui,
    author = {Emde, A and Schulz, Marcel H and Weese, David and Sun, Ruping and Vingron, Martin and Kalscheuer, Vera M and Haas, Stefan A and Reinert, Knut},
    title = {{Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS}},
    journal = {Bioinformatics (Oxford, England)},
    year = {2012},
    volume = {28},
    number = {5},
    pages = {619--627},
    month = mar,
    publisher = {Oxford University Press},
    affiliation = {Department of Computer Science, Freie Universit{"a}t Berlin, Takustrasse 9, Max-Planck-Institute for Molecular Genetics, Berlin, Germany. emde@inf.fu-berlin.de},
    doi = {10.1093/bioinformatics/bts019},
    pmid = {22238266},
    language = {English},
    read = {Yes},
    rating = {5},
    date-added = {2012-01-24T21:49:19GMT},
    date-modified = {2016-01-14T20:10:20GMT},
    abstract = {MOTIVATION:The reliable detection of genomic variation in resequencing data is still a major challenge, especially for variants larger than a few base pairs. Sequencing reads crossing boundaries of structural variation carry the potential for their identification, but are difficult to map.
    RESULTS:Here we present a method for 'split' read mapping, where prefix and suffix match of a read may be interrupted by a longer gap in the read-to-reference alignment. We use this method to accurately detect medium-sized insertions and long deletions with precise breakpoints in genomic resequencing data. Compared with alternative split mapping methods, SplazerS significantly improves sensitivity for detecting large indel events, especially in variant-rich regions. Our method is robust in the presence of sequencing errors as well as alignment errors due to genomic mutations/divergence, and can be used on reads of variable lengths. Our analysis shows that SplazerS is a versatile tool applicable to unanchored or single-end as well as anchored paired-end reads. In addition, application of SplazerS to targeted resequencing data led to the interesting discovery of a complete, possibly functional gene retrocopy variant.
    AVAILABILITY:SplazerS is available from http://www.seqan.de/projects/ splazers.
    SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.},
    url = {http://bioinformatics.oxfordjournals.org/content/28/5/619.full},
    local-url = {file://localhost/Users/reinert/Dropbox/Library.papers3/Articles/2012/Emde/Bioinformatics%202012%20Emde.pdf},
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    uri = {url{papers3://publication/doi/10.1093/bioinformatics/bts019}}
    }
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