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Circlator: automated circularization of genome assemblies using long sequencing reads.

Genome biology | Dec 29, 2015

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/ .

Pubmed ID: 26714481 RIS Download

Mesh terms: Contig Mapping | DNA, Circular | Genome, Bacterial | Genome, Mitochondrial | Genome, Protozoan | Humans | Plasmodium falciparum | Software

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This is a list of tools and resources that we have found mentioned in this publication.


Circlator

Software that automates assembly circularization and produces accurate linear representations of circular sequences. It is used for assembling of DNA sequence data of complete bacterial and small eukaryotic genomes.

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Prodigal

A microbial (bacterial and archaeal) gene finding software program developed at Oak Ridge National Laboratory and the University of Tennessee.

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