CGAT: computational genomics analysis toolkit

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  • David Sims
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
  • Nicholas E. Ilott
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
  • Stephen N. Sansom
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
  • Ian M. Sudbery
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
  • Jethro S. Johnson
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
  • Katherine A. Fawcett
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
  • Antonio J. Berlanga-Taylor
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
  • Sebastian Luna-Valero
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
  • Chris P. Ponting
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
  • Andreas Heger
    CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK

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Description

<jats:title>Abstract</jats:title> <jats:p>Summary: Computational genomics seeks to draw biological inferences from genomic datasets, often by integrating and contextualizing next-generation sequencing data. CGAT provides an extensive suite of tools designed to assist in the analysis of genome scale data from a range of standard file formats. The toolkit enables filtering, comparison, conversion, summarization and annotation of genomic intervals, gene sets and sequences. The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy.</jats:p> <jats:p>Availability: The toolkit is freely available from http://github.com/CGATOxford/cgat</jats:p> <jats:p>Contact:  andreas.heger@dpag.ox.ac.uk</jats:p>

Journal

  • Bioinformatics

    Bioinformatics 30 (9), 1290-1291, 2014-01-05

    Oxford University Press (OUP)

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