Bacterial Whole-Genome De Novo Sequencing

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Bacterial Whole-Genome De Novo Sequencing

CD Genomics is providing long-read sequencing technologies developed by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) to fully support the de novo assembly of bacterial genomes. To ensure maximum assembly accuracy, we recommend using short-read Illumina data to further polish the genome assembly. Our services are end-to-end and customized, enabling the rapid delivery of more cost-effective strategies and high-quality genome assemblies.

Using Long-Read Sequencing to Improve De Novo Assembly of Bacterial Genomes

Rod-shaped and spherical bacteria on skin or mucous membrane.

Short-read sequencing technologies, such as the Illumina platform, are now widely used in bacterial genome research due to its ability to provide rapid and accurate analysis of the entire bacterial genome. However, short-read sequencing, in addition to being limited by amplification and sequencing bias, has inherent limitations that generally do not allow for whole-genome assembly. Long-read sequencing technologies developed by ONT and PacBio can produce long reads in tens of kilobase pairs, thus overcoming the limitations of short-read sequencing to obtain a complete assembly. As the first established long-read technology, PacBio Single Molecular Real-Time (SMRT) sequencing is based on a sequencing-by-synthesis method. The PacBio sequencer can generate the average length of reads ranging from 10-14 kb and can reach throughputs of about 30 Gb per run. ONT long-read sequencing has no upper read length limit and can assemble the complete microbial genome relatively quickly and inexpensively, which has gained increasing popularity. This technique has been used to assist in the completion of the genome sequence of Staphylococcus aureus. With the advanced technologies and improved analysis pipelines, ONT long-read sequencing can be applied for complex bacteria, such as Fusobacterium nucleatum, Pseudomonas koreensis, Mycobacterium tuberculosis and other genomes with long repetitive sequences.

Service Highlights

  • Years of experience in microbial de novo sequencing projects, including bacterial genomes.
  • Facilitating high-quality genome reconstruction with the largest short and long-read sequencing capacity.
  • Providing complete and customized solutions for in-depth analysis of bacterial genomes.
  • Generation accurate reference sequences, even for complicated bacterial genomes.

Bacterial Whole-Genome De Novo Sequencing Service Overview

Sequencing Platform Illumina HiSeq PE150 PacBio Sequel ll Nanopore PromethION
Sample Requirements Sample Type: genomic DNA
Amount:≥ 200ng
no degradation and no contamination
Sample Type: HMW genomic DNA
Amount:≥ 15μg
Fragments should be  ≥ 20 kb
Sample Type: HMW genomic DNA
Amount:≥ 10μg
Fragments should be  ≥ 20 kb
Sequencing Strategies 350 bp insert library, ≥ 50 X 20Kb SMRTbell library, CLR sequencing, ≥100X ONT Library preparation, ≥100X
Application Scope Large-scale sequencing and rapid scanning Sequencing of a small number of strains
Accuracy in place
Sequencing of a small number of strains
Accuracy in place
Delivery Cycle Minimum of 30 working days Minimum of 45 working days Minimum of 40 working days

Workflow of Our Services

Workflow of Our Services-CD Genomics.

Analysis Contents

Analysis of bacterial genome information at different levels of fineness, deciphering the development of bacteria, and exploring their potential value. Our analysis consists of two main parts: standard analysis and advanced analysis. Specific analytical services are as follows, but are not limited to,

  • Standard analysis
    -Data quality control.
    -Genome assembly and evaluation of assembly results.
    -Genome component analysis.
    -Gene functional annotation.
    -Genome cycle graph generation.
  • Advanced analysis
    -Comparative genome analysis.
    -Genome island prediction.
    -Prophage prediction.
    -Bacterial virulence-related gene annotation.
    -Bacterial drug-resistance gene annotation.
    -Phylogenetic analysis.

To perform bacterial whole-genome de novo sequencing, researchers choose CD Genomics. With multiple specialists and years of experience in this field, we guarantee you high-quality data and integrated bioinformatics analyses. Please feel free to contact us. We are happy to help you!


  1. Zhang, P., et al. (2021). Comparison of de novo assembly strategies for bacterial genomes. International Journal of Molecular Sciences, 22(14), 7668.
  2. Liao, Y. C., et al. (2019). Completing circular bacterial genomes with assembly complexity by using a sampling strategy from a single MinION run with barcoding. Frontiers in microbiology, 2068.
For Research Use Only. Not for use in diagnostic procedures.

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