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  • MOSAIK: a hash-based algori... MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping
    Lee, Wan-Ping; Stromberg, Michael P; Ward, Alistair ... PloS one, 03/2014, Volume: 9, Issue: 3
    Journal Article
    Peer reviewed
    Open access

    MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads ...
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  • SSW library: an SIMD Smith-... SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications
    Zhao, Mengyao; Lee, Wan-Ping; Garrison, Erik P ... PloS one, 12/2013, Volume: 8, Issue: 12
    Journal Article
    Peer reviewed
    Open access

    The Smith-Waterman algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools ...
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  • Genome graphs and the evolu... Genome graphs and the evolution of genome inference
    Paten, Benedict; Novak, Adam M; Eizenga, Jordan M ... Genome research, 05/2017, Volume: 27, Issue: 5
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    Open access

    The human reference genome is part of the foundation of modern human biology and a monumental scientific achievement. However, because it excludes a great deal of common human variation, it ...
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  • SpeedSeq: ultra-fast person... SpeedSeq: ultra-fast personal genome analysis and interpretation
    Chiang, Colby; Layer, Ryan M; Faust, Gregory G ... Nature methods, 10/2015, Volume: 12, Issue: 10
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    Peer reviewed
    Open access

    SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a ...
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  • BamTools: a C++ API and too... BamTools: a C++ API and toolkit for analyzing and managing BAM files
    BARNETT, Derek W; GARRISON, Erik K; QUINLAN, Aaron R ... Bioinformatics (Oxford, England), 06/2011, Volume: 27, Issue: 12
    Journal Article
    Peer reviewed
    Open access

    Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous ...
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  • Variation graph toolkit imp... Variation graph toolkit improves read mapping by representing genetic variation in the reference
    Garrison, Erik; Sirén, Jouni; Novak, Adam M ... Nature biotechnology, 10/2018, Volume: 36, Issue: 9
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    Reference genomes guide our interpretation of DNA sequence data. However, conventional linear references represent only one version of each locus, ignoring variation in the population. Poor ...
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  • Haplotype-aware graph indexes Haplotype-aware graph indexes
    Sirén, Jouni; Garrison, Erik; Novak, Adam M ... Bioinformatics, 01/2020, Volume: 36, Issue: 2
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    Open access

    Abstract Motivation The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely ...
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  • Genotyping structural varia... Genotyping structural variants in pangenome graphs using the vg toolkit
    Hickey, Glenn; Heller, David; Monlong, Jean ... Genome Biology, 02/2020, Volume: 21, Issue: 1
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    Open access

    Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, ...
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  • Removing reference bias and... Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph
    Martiniano, Rui; Garrison, Erik; Jones, Eppie R ... Genome Biology, 09/2020, Volume: 21, Issue: 1
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    During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules ...
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  • Nanopore sequencing and the... Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
    Shafin, Kishwar; Pesout, Trevor; Lorig-Roach, Ryan ... Nature biotechnology, 09/2020, Volume: 38, Issue: 9
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    De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, ...
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