Oxford Nanopore Sequencing Data Analysis

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Oxford Nanopore Sequencing Data Analysis

AGCT bases.

Oxford Nanopore Sequencing Technology (ONT) enables real-time sequencing of native strands of interest without optics or amplification, and its data has been shown to efficiently and cost-effectively improve de novo genome assemblies, structural genomic variants, and more. So far, this long-read sequencing has been applied in genomic analysis, identification of pathogens, metagenomic environmental monitoring, food safety monitoring, and other aspects of life sciences. To meet the growing demand for sequencing data analysis, CD Genomics offers Nanopore sequencing data analysis as part of our unique portfolio of comprehensive services for long-read sequencing bioinformatics analysis. We are dedicated to providing long-read sequencing data analysis in a wide range of fields, including the pharmaceutical and biotechnology industries, as well as scientific and agricultural research.

Nanopore Sequencing Data Analysis at CD Genomics

Our Nanopore sequencing analysis workflow typically consists of five steps, ranging from raw data preprocessing, data quality control(QC), and data analysis, to analytical report delivery. Data analysis can be further divided into two parts, including primary data, such as alignment with the reference genome, classification, and secondary data analysis, such as assembly, expression, and variant calling. We perform data analysis at the level of bioinformatics expertise, providing appropriate solutions at each stage.

Workflow of Our Service

Workflow of Our Service

Analyze and Make the Most of Your Data

  • Base-calling (Guppy, Bonito)
  • Nanopore long-read data pre-processing. (Porechop, NanoFilt)
  • Reference-based alignment (Minimap2).
  • De novo genome assembly (Flye, Redbean, Shasta, Racon).
  • Assessment (QUAST/BUSCO) and polishing of genome assembly (Nanopolish, MarginPolish/HELEN).
  • Structural variant detection (NGMLR, sniffles, cuteSV, SURVIVOR, IGV).
  • RNA analysis, such as fusion gene detection (JAFFAL).
  • Epigenetic base modifications and methylation. (Guppy, Nanopolish)
  • Metagenomics, including homolog identification and phylogenetic analysis (Kraken, kaiju).

Benefits of Our Service

DNA sequencing analysis software on a laptop from the genetic engineering Lab.

  • Multiple analysis tools for different types of Nanopore sequencing data.
  • Robust and customized analytical workflows.
  • Dedicated bioinformaticians with extensive experience in long-read sequence data analysis.
  • Provide intuitive, easy-to-use, and complete analytical study reports.
  • Fast turnaround time with the most competitive prices.

As one of the largest providers of long-read sequencing services, CD Genomics continues to equip itself with the latest algorithms and methods to meet the rapidly evolving and ever-advancing field of long-read sequencing. Thank you for your interest in our services. Please contact us for more information about our services. We are glad to cooperate with you!

Related Services


  1. de Koning, W., et al. (2020). "NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy." GigaScience, 9(10), giaa105.
  2. Davidson, N. M., et al. (2022). "JAFFAL: detecting fusion genes with long-read transcriptome sequencing." Genome biology, 23(1), 1-20.
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