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Related Experiment Video

Updated: Jan 19, 2026

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

Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run

Yu-Chieh Liao¹, Hung-Wei Cheng¹, Han-Chieh Wu²

¹Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan.

Frontiers in Microbiology

|September 26, 2019

Summary

This summary is machine-generated.

CCBGpipe automates the reconstruction of complete circular bacterial genomes using Oxford Nanopore MinION sequencing data. This pipeline facilitates accurate genome assembly and analysis for various bacterial species.

Keywords:

MinION sequencing assembly complexity bacterial genome de novo assembly one-stop analysis

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Last Updated: Jan 19, 2026

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

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Published on: August 20, 2021

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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 and Bioinformatics
Microbial Genomics
DNA Sequencing Technology

Background:

Oxford Nanopore MinION offers long reads for bacterial genome assembly.
Existing tools lack a unified pipeline for automated circular bacterial genome reconstruction.
Accurate assembly of bacterial chromosomes and plasmids is crucial for understanding microbial biology.

Purpose of the Study:

To present CCBGpipe, an automated pipeline for complete circular bacterial genome reconstruction.
To enable one-stop analysis of bacterial genomes using MinION sequencing data.
To facilitate the assembly and characterization of bacterial chromosomes and plasmids.

Main Methods:

Demultiplexing and base calling of raw nanopore current signals.
Iterative de novo assembly using a sampling strategy to generate circular contigs.
Polishing of circular contigs with raw signals and reads, followed by linearization and rearrangement based on replication origins (e.g., dnaA/repA) and GC skew.

Main Results:

CCBGpipe successfully assembled 48 circular sequences (12 chromosomes, 36 plasmids) from 12 bacterial species, including Acinetobacter nosocomialis, Acinetobacter pittii, and Staphylococcus aureus.
The pipeline achieved complete circular genome reconstruction from a single MinION run with sufficient sequencing depth (80×).
Demonstrated automated and accurate assembly of bacterial chromosomes and plasmids.

Conclusions:

CCBGpipe provides a comprehensive and automated solution for circular bacterial genome assembly.
The pipeline leverages long-read sequencing data for high-quality genome reconstruction.
CCBGpipe is a valuable tool for microbial genomics research, enabling efficient analysis of bacterial genomes.