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.

doi:10.1186/s13059-015-0849-0

Cited by 816 publications

(604 citation statements)

References 26 publications

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“…Expected genome size was set to 4,800,000 bp [as indicated by an HGAP 3 trial run (data not shown)]. This approach resulted in two contigs (with mean QV score at 48.8 and 47.7, respectively) that were subsequently circularized by Circlator 0.16.0 (Hunt et al, 2015) using corrected sub-reads generated by HGAP 2 (with 6,000 minimum seed read length). The ‘RS_Resequencing.1’ protocol on SMRT ® Analysis was then used to align raw reads to the circularized genome for an improved consensus.…”

Section: Methodsmentioning

confidence: 99%

Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef

Gunn

Brennan

et al. 2016

Front. Microbiol.

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Blown pack spoilage (BPS) is a major issue for the beef industry. Etiological agents of BPS involve members of a group of Clostridium species, including Clostridium estertheticum which has the ability to produce gas, mostly carbon dioxide, under anaerobic psychotrophic growth conditions. This spore-forming bacterium grows slowly under laboratory conditions, and it can take up to 3 months to produce a workable culture. These characteristics have limited the study of this commercially challenging bacterium. Consequently information on this bacterium is limited and no effective controls are currently available to confidently detect and manage this production risk. In this study the complete genome of C. estertheticum DSM 8809 was determined by SMRT® sequencing. The genome consists of a circular chromosome of 4.7 Mbp along with a single plasmid carrying a potential tellurite resistance gene tehB and a Tn3-like resolvase-encoding gene tnpR. The genome sequence was searched for central metabolic pathways that would support its biochemical profile and several enzymes contributing to this phenotype were identified. Several putative antibiotic/biocide/metal resistance-encoding genes and virulence factors were also identified in the genome, a feature that requires further research. The availability of the genome sequence will provide a basic blueprint from which to develop valuable biomarkers that could support and improve the detection and control of this bacterium along the beef production chain.

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Section: Methodsmentioning

confidence: 99%

Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef

Gunn

Brennan

et al. 2016

Front. Microbiol.

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“…The resultant contigs were checked for further joins and circularity using Circlator version 1.5 (10). Contigs were polished using Quiver, part of the SMRT Analysis suite version 2.3 (Pacific Biosciences) (11), and the sequence order was verified using the restriction enzyme AflII for whole-genome mapping (OpGen, Gaithersburg, MD, USA).…”

Section: Genome Announcementmentioning

confidence: 99%

Genome Sequence of a Multidrug-Resistant Candida haemulonii Isolate from a Patient with Chronic Leg Ulcers in Israel

et al. 2018

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“…The current NCTC manual assembly pipeline uses the HGAP assembler (Chin et al 2013) to produce a list of contigs, and Circlator (Hunt et al 2015) to circularize contigs. The assembly graphs produced by HINGE with no parameter tuning for each of these data sets are available online (http://web.stanford.edu/ gkamath/NCTC/report.html) and in Supplemental Table S4, along with the contig statistics of the NCTC pipeline results and the assembly graph produced by Miniasm (Li 2016).…”

Section: Evaluation On the Nctc Databasementioning

confidence: 99%

HINGE: long-read assembly achieves optimal repeat resolution

et al. 2017

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Long-read sequencing technologies have the potential to produce gold-standard de novo genome assemblies, but fully exploiting error-prone reads to resolve repeats remains a challenge. Aggressive approaches to repeat resolution often produce misassemblies, and conservative approaches lead to unnecessary fragmentation. We present HINGE, an assembler that seeks to achieve optimal repeat resolution by distinguishing repeats that can be resolved given the data from those that cannot. This is accomplished by adding "hinges" to reads for constructing an overlap graph where only unresolvable repeats are merged. As a result, HINGE combines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de Bruijn graph assemblers. HINGE was evaluated on the long-read bacterial data sets from the NCTC project. HINGE produces more finished assemblies than Miniasm and the manual pipeline of NCTC based on the HGAP assembler and Circlator. HINGE also allows us to identify 40 data sets where unresolvable repeats prevent the reliable construction of a unique finished assembly. In these cases, HINGE outputs a visually interpretable assembly graph that encodes all possible finished assemblies consistent with the reads, while other approaches such as the NCTC pipeline and FALCON either fragment the assembly or resolve the ambiguity arbitrarily.

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Circlator: automated circularization of genome assemblies using long sequencing reads

Cited by 816 publications

References 26 publications

Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef

Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef

Genome Sequence of a Multidrug-Resistant Candida haemulonii Isolate from a Patient with Chronic Leg Ulcers in Israel

HINGE: long-read assembly achieves optimal repeat resolution

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