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)

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, Professor 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 > School of Infection & Immunity
• 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