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Genome Annotation and Assembly

Genome Annotation and Assembly

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.

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Related Experiment Video

Updated: Sep 9, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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

Autocycler: long-read consensus assembly for bacterial genomes.

Ryan R Wick^1,2, Benjamin P Howden^1,2, Timothy P Stinear^1,2

¹Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia.

Bioinformatics (Oxford, England)

|August 28, 2025

Summary

Autocycler is a new automated tool that generates accurate bacterial genome assemblies from long-read sequencing data. It outperforms existing methods, offering improved sequence and structural accuracy for bacterial genomics.

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Last Updated: Sep 9, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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

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Published on: December 26, 2018

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

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Published on: April 14, 2016

Area of Science:

Genomics
Bioinformatics
Microbial Ecology

Background:

Long-read sequencing facilitates complete bacterial genome assembly but assemblers have limitations.
Current consensus assembly methods like Trycycler lack automation, hindering scalability.
A need exists for automated, high-quality bacterial genome assembly from long-read data.

Purpose of the Study:

To develop an automated tool for generating accurate bacterial genome assemblies.
To improve upon existing consensus assembly methods for long-read sequencing data.

Main Methods:

Autocycler combines multiple alternative long-read assemblies.
It builds a De Bruijn graph, clusters and filters contigs, and resolves consensus sequences.
The tool supports optional manual curation for refined assemblies.

Main Results:

Autocycler produced bacterial genome assemblies with lower error rates.
The tool demonstrated improved structural accuracy compared to individual assemblers and other consensus methods.
Evaluation used Oxford Nanopore Technologies reads from five bacterial isolates.

Conclusions:

Autocycler provides an automated and accurate solution for bacterial genome assembly.
The tool enhances the utility of long-read sequencing for microbial genomics.
Autocycler represents a significant advancement in automated genome assembly pipelines.