Circlator: automated circularization of genome assemblies using long sequencing reads

Hunt, M., Silva, N. D., Otto, T. D. , Parkhill, J., Keane, J. A. and Harris, S. R. (2015) Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biology, 16, 294. (doi: 10.1186/s13059-015-0849-0) (PMID:26714481) (PMCID:PMC4699355)

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Abstract

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/ .

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Authors: Hunt, M., Silva, N. D., Otto, T. D., Parkhill, J., Keane, J. A., and Harris, S. R.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Genome Biology
Publisher:BioMed Central
ISSN:1465-6906
ISSN (Online):1474-760X
Copyright Holders:Copyright ©2015 The Authors
First Published:First published in Genome Biology 16:294
Publisher Policy:Reproduced under a Creative Commons License

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