Related Experiment Video
Updated: Mar 28, 2026
12:08
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
6.0K
Circlator: automated circularization of genome assemblies using long sequencing reads
Martin Hunt1, Nishadi De Silva2, Thomas D Otto2
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK. mh12@sanger.ac.uk.
Genome Biology
|December 31, 2015
Summary
Circlator automates the circularization of DNA sequences, a crucial step for complete genome assembly. This tool accurately represents circular DNA, including bacterial chromosomes and plasmids, using long-read sequencing data.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Advancements in DNA sequencing technologies enable the assembly of large genomic fragments.
- Completing the assembly of bacterial and small eukaryotic genomes is hindered by the challenge of circularizing sequences.
Purpose of the Study:
- To present Circlator, a novel computational tool designed to automate the DNA sequence assembly circularization process.
- To provide accurate linear representations of circular DNA sequences.
Main Methods:
- Development and application of the Circlator software tool.
- Utilizing long-read sequencing data from Pacific Biosciences and Oxford Nanopore platforms.
- Testing Circlator on diverse circularizable sequences, including bacterial chromosomes, plasmids, and organelle genomes.
Main Results:
- Circlator successfully circularized 26 out of 27 tested circularizable sequences.
- The tool demonstrated accuracy in representing circular DNA, including 11 bacterial chromosomes and 12 plasmids.
- Successful circularization was also achieved for the apicoplast and mitochondrion of Plasmodium falciparum and a human mitochondrion.
Conclusions:
- Circlator is the first tool to automate DNA sequence assembly circularization.
- The software provides accurate linear representations of circular sequences, essential for complete genome assembly.
- Circlator is a valuable tool for researchers working with long-read sequencing data and aiming for complete genome reconstructions.
Related Concept Videos
03:36Genome Annotation and Assembly
21.5K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
21.5K
03:21RNA-seq
12.5K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
12.5K
03:00Next-generation Sequencing
100.9K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
100.9K
01:57Sanger Sequencing
778.3K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
778.3K