Circlator: automated circularization of genome assemblies using long sequencing reads

The assembly of DNA sequence data is undergoing a renaissance thanks to emerging technologies capable of producing reads tens of kilobases long. Assembling complete bacterial and small eukaryotic genomes is now possible, but the final step of circularizing sequences remains unsolved. Here we present...

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Detalles Bibliográficos
Autores principales: Hunt, Martin, Silva, Nishadi De, Otto, Thomas D., Parkhill, Julian, Keane, Jacqueline A., Harris, Simon R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4699355/
https://www.ncbi.nlm.nih.gov/pubmed/26714481
http://dx.doi.org/10.1186/s13059-015-0849-0
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author Hunt, Martin
Silva, Nishadi De
Otto, Thomas D.
Parkhill, Julian
Keane, Jacqueline A.
Harris, Simon R.
author_facet Hunt, Martin
Silva, Nishadi De
Otto, Thomas D.
Parkhill, Julian
Keane, Jacqueline A.
Harris, Simon R.
author_sort Hunt, Martin
collection PubMed
description The assembly of DNA sequence data is undergoing a renaissance thanks to emerging technologies capable of producing reads tens of kilobases long. 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 representations 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/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0849-0) contains supplementary material, which is available to authorized users.
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spelling pubmed-46993552016-01-05 Circlator: automated circularization of genome assemblies using long sequencing reads Hunt, Martin Silva, Nishadi De Otto, Thomas D. Parkhill, Julian Keane, Jacqueline A. Harris, Simon R. Genome Biol Method The assembly of DNA sequence data is undergoing a renaissance thanks to emerging technologies capable of producing reads tens of kilobases long. 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 representations 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/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0849-0) contains supplementary material, which is available to authorized users. BioMed Central 2015-12-29 2015 /pmc/articles/PMC4699355/ /pubmed/26714481 http://dx.doi.org/10.1186/s13059-015-0849-0 Text en © Hunt et al. 2015 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Hunt, Martin
Silva, Nishadi De
Otto, Thomas D.
Parkhill, Julian
Keane, Jacqueline A.
Harris, Simon R.
Circlator: automated circularization of genome assemblies using long sequencing reads
title Circlator: automated circularization of genome assemblies using long sequencing reads
title_full Circlator: automated circularization of genome assemblies using long sequencing reads
title_fullStr Circlator: automated circularization of genome assemblies using long sequencing reads
title_full_unstemmed Circlator: automated circularization of genome assemblies using long sequencing reads
title_short Circlator: automated circularization of genome assemblies using long sequencing reads
title_sort circlator: automated circularization of genome assemblies using long sequencing reads
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4699355/
https://www.ncbi.nlm.nih.gov/pubmed/26714481
http://dx.doi.org/10.1186/s13059-015-0849-0
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