Circlator: automated circularization of genome assemblies using long sequencing reads
By Martin Hunt, Nishadi De Silva, Thomas D. Otto, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris. Genome Biology, 2015
1,076 citations recorded by the source corpus.
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/.
Subfields: Ecology, Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/749d85300df429f647ae3e0946cb7ceae95bb78d
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Citations in the corpus
- MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies (2018, positive): “Optionally, the minimus2 tool provided by Circlator [26] is run on the assembly to determine if any contigs have overlapping ends.”
- Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads (2016, methodology): “These must be repaired manually or with a tool such as Circla-tor[47].”