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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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Updated: May 12, 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

Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies.

Hewei Liang^1,2,3, Yuanqiang Zou^3,4, Mengmeng Wang^1,5

¹BGI Research, Shenzhen 518083, China.

Gigabyte (Hong Kong, China)

|May 7, 2025

Summary

This summary is machine-generated.

CycloneSEQ long-read sequencing, combined with DNBSEQ short-reads, enables high-quality, complete circular genome assemblies. This hybrid approach overcomes limitations of short-read sequencing for microbial genomics.

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Last Updated: May 12, 2025

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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Published on: October 23, 2013

Area of Science:

Microbial genomics
Next-generation sequencing technologies

Background:

Short-read sequencing platforms (Illumina, DNBSEQ) are cost-effective but yield fragmented draft genomes.
Limitations in assembling complete microbial genomes hinder comprehensive analysis.

Purpose of the Study:

To evaluate CycloneSEQ long-read sequencing for assembling complete circular microbial genomes.
To assess the efficacy of hybrid assembly combining long-reads and short-reads.

Main Methods:

Utilized CycloneSEQ for long-read sequencing (average length 11.6 kbp).
Performed hybrid assembly integrating CycloneSEQ long-reads with DNBSEQ short-reads.
Validated the method across nine microbial species.

Main Results:

Achieved highly accurate hybrid assemblies with low error rates (0.04 mismatches, 0.08 indels per 100 kbp) compared to reference genomes.
Successfully assembled complete circular genomes, including multi-copy rRNA genes, which are challenging for short-reads alone.
Determined optimal data requirements: >500 Mbp short-read data with 100 Mbp long-read data for high-quality assemblies.

Conclusions:

CycloneSEQ long-reads significantly enhance genome completeness and accuracy in hybrid assembly.
The hybrid approach is effective for assembling complete circular genomes from microbial communities.
Further improvement in CycloneSEQ base quality is recommended, while DNBSEQ integration boosts overall accuracy.