38 research outputs found

    Tailoring r-index for Document Listing Towards Metagenomics Applications

    Get PDF
    A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of a set of species with each species represented by its highly similar strains. It has been recently shown that accurate read assignment can be achieved with k-mer hashing-based pseudoalignment: a read is assigned to species A if each of its k-mer hits to a reference collection is located only on strains of A. We study the underlying primitives required in pseudoalignment and related tasks. We propose three space-efficient solutions building upon the document listing with frequencies problem. All the solutions use an r-index (Gagie et al., SODA 2018) as an underlying index structure for the text obtained as concatenation of the set of species, as well as for each species. Given t species whose concatenation length is n, and whose Burrows-Wheeler transform contains r runs, our first solution, based on a grammar-compressed document array with precomputed queries at non terminal symbols, reports the frequencies for the distinct documents in which the pattern of length m occurs in time. Our second solution is also based on a grammar-compressed document array, but enhanced with bitvectors and reports the frequencies in time, over a machine with wordsize w. Our third solution, based on the interleaved LCP array, answers the same query in time. We implemented our solutions and tested them on real-world and synthetic datasets. The results show that all the solutions are fast on highly-repetitive data, and the size overhead introduced by the indexes are comparable with the size of the r-index.Peer reviewe

    The Neutron star Interior Composition Explorer (NICER): design and development

    Get PDF

    The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

    Get PDF
    The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

    Search for single production of vector-like quarks decaying into Wb in pp collisions at s=8\sqrt{s} = 8 TeV with the ATLAS detector

    Get PDF

    Measurement of the charge asymmetry in top-quark pair production in the lepton-plus-jets final state in pp collision data at s=8TeV\sqrt{s}=8\,\mathrm TeV{} with the ATLAS detector

    Get PDF

    Measurement of the bbb\overline{b} dijet cross section in pp collisions at s=7\sqrt{s} = 7 TeV with the ATLAS detector

    Get PDF

    ATLAS Run 1 searches for direct pair production of third-generation squarks at the Large Hadron Collider

    Get PDF

    Search for dark matter in association with a Higgs boson decaying to bb-quarks in pppp collisions at s=13\sqrt s=13 TeV with the ATLAS detector

    Get PDF

    Charged-particle distributions at low transverse momentum in s=13\sqrt{s} = 13 TeV pppp interactions measured with the ATLAS detector at the LHC

    Get PDF
    corecore