Tell Us About Your Project

We are dedicated to providing outstanding customer service and being reachable at all times.

Request a Quote

Nanopore-Based Microbial Genome Sequencing

Inquiry      >

We offer microbial genome analysis based on nanopore sequencing from the Oxford Nanopore Technologies (ONT) to identify DNA bases by measuring the changes in electrical conductivity as DNA strands pass through a biological pore. We are dedicated to ensuring long and unbiased sequence reads for microbial whole-genome assembly and analysis, without amplification or chemical reactions.

Our Advantages:
  • High-throughput, low cost, and long-read sequencing.
  • Real-time sequencing directly targeting single DNA molecules.
  • Time-saving, simplified workflow.
  • Flexible bioinformatics pipelines.
  • Fast turnaround times and a highly experienced expert team.
Tell Us About Your Project

We are dedicated to providing outstanding customer service and being reachable at all times.

Request a Quote

Nanopore-based genome analysis platform

In recent years, there have been enormous achievements made in the DNA sequencing technologies, including the next-generation sequencing (NGS), 3rd-generation sequencing (also known as long-read sequencing), and the corresponding innovations in bioinformatics analysis. Those achievements are driving the development of an exciting field of biological research called the genome analysis. Oxford nanopore sequencing identifies DNA bases by measuring the current changes in electrical conductivity as nucleic acid molecules pass through a biological pore in membranes, generating much longer average reads (ultra-long reads, over 800,000 bases) than other DNA sequencing technologies. Our nanopore-based microbial genomics analysis can generate ultra-long reads (about 5.4 kb to 10 kb of average read length) that span challenging genomic regions. We also polish the microbial genome assembly with short reads generated by the Illumina system to improve accuracy to 99.96%.

Our nanopore-based microbial genome analysis services include microbial whole-genome sequencing and targeted sequencing, along with comprehensive bioinformatics tools to reconstruct bacterial, fungal, or viral genomes (de novo) and perform further genome-based analysis. The highly precise and complete genome assemblies enable the accurate microbial identification, genome structure evaluation, variants (phage insertion, transposon insertion, SVs, InDels, SNVs) identification along the evolution of virulence, understanding of the role of mobile elements in drug transmission and resistance, and gene function annotation. We are dedicated to helping you generate high-quality, closed-reference genomes, redefining the extent of genetic diversity and elucidating microbial genetics and evolution.

Nanopore-based microbial genome analysis workflow

Bioinformatics Analysis

Our bioinformatics analysis includes raw data quality control, genome assembly and polishing, genome annotation and analysis, comparative analysis, and custom analysis.

Pipelines Details
Raw data quality control Correction, classification, reduced redundancy, etc.
Genome assembly and polishing Reveals genomics sequence, gene structure and location.
Genome annotation and analysis Prediction of pathogenicity genes, susceptibility genes, and non-coding RNAs, detection of clustered regularly interspaced short palindromic repeats (CRISPRs), etc.
Comparative genomics Phylogenetic analyses, divergence-time estimation, etc.
Custom analyses More data mining upon your request

Sample Requirement

    1. DNA amount ≥ 5 µg, concentration ≥ 100 ng/µL, 1.8 < OD260/280 < 2.0,2.0 < OD260/230 < 2.2
    2. No detergents or surfactants in the buffer, 10 mM TRIS (pH=8.0-8.4) is recommended.

Sampling kits: We provide a range of microbial sampling kits for clients, including MicroCollect™ oral sample microbial collection products and MicroCollect™ stool sample collection products.

Deliverables: Raw sequencing data (FASTQ), trimmed and stitched sequences, quality-control dashboard, statistic data, and your designated bioinformatics report.


  1. Xinpeng Tian, et al. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level. Frontiers in Microbiology. 2016, 7: 998-1104.
  2. Hans J. Jansen, et al. Rapid de novo assembly of the European eel genome from nanopore sequencing reads. SCIENTIFIC REPORTS. 2017, 7: 7213.
  3. Miten Jain, et al. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biology. 2016, 17:239.
* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.

Featured Resources
Copyright © 2024 CD Genomics. All rights reserved. Terms of Use | Privacy Notice