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Circlator: automated circularization of genome assemblies using long sequencing reads

Martin Hunt, Nishadi De Silva, Thomas D Otto, Julian Parkhill, Jacqueline A Keane, Simon R Harris
doi: https://doi.org/10.1101/023408
Martin Hunt
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
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  • For correspondence: mh12@sanger.ac.uk sh16@sanger.ac.uk
Nishadi De Silva
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
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Thomas D Otto
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
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Julian Parkhill
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
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Jacqueline A Keane
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
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Simon R Harris
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
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  • For correspondence: mh12@sanger.ac.uk sh16@sanger.ac.uk
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Abstract

The assembly of DNA sequence data into finished genomes is undergoing a renais-sance thanks to emerging technologies producing reads of tens of kilobases. Assembling complete bacterial and small eukaryotic genomes is now possible, but the final step of circularizing sequences remains unsolved. Here we present Circlator, the first tool to automate assembly circularization and produce accurate linear rep-resentations of circular sequences. Using Pacific Biosciences and Oxford Nanopore data, Circlator correctly circularized 26 of 27 circularizable sequences, comprising 11 chromosomes and 12 plasmids from bacteria, the apicoplast and mitochondrion of Plasmodium falciparum and a human mitochondrion. Circlator is available at http://sanger-pathogens.github.io/circlator/.

  • List of abbreviations

    NCTC
    National Collection of Type Cultures
    ONT
    Oxford Nanopore Technologies
    PacBio
    Pacific Biosciences
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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    Posted July 28, 2015.
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    Circlator: automated circularization of genome assemblies using long sequencing reads
    Martin Hunt, Nishadi De Silva, Thomas D Otto, Julian Parkhill, Jacqueline A Keane, Simon R Harris
    bioRxiv 023408; doi: https://doi.org/10.1101/023408
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    Circlator: automated circularization of genome assemblies using long sequencing reads
    Martin Hunt, Nishadi De Silva, Thomas D Otto, Julian Parkhill, Jacqueline A Keane, Simon R Harris
    bioRxiv 023408; doi: https://doi.org/10.1101/023408

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