Copy Number Analysis

With years of experience, CD Genomics provides professional analysis services for microbial identification and characterization. Specifically, we offer copy number analysis of microorganisms, a part of our complete solutions for microbial characterization. Our NGS and long-read sequencing platforms ensure accurate, comprehensive microbial genomics analysis.

Our Advantages:
  • Standardized laboratory methods and quality assurance processes.
  • Advanced genomics solutions and bioinformatics analysis.
  • Stand at the frontiers of microbial strain characterization.
  • Next-generation sequencing and long-read sequencing platforms.
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Introduction to copy number analysis

Microorganisms are widely used in large-scale industrial processes to produce a variety of metabolites, like lactic acid and ethanol. Many laboratories and bio-industries need to characterize microbial strains to make better use of microorganisms. Microorganisms can contain multiple copies of a gene, cassette or operon, which can be found especially in fungi. The number of gene copy may affect the expression levels of the corresponding proteins and provides valuable insights into production strain optimization. Transgenic models are very useful, but transgenes typically insert randomly in the genome and the number of copies varies, leading to copy number variations (CNVs). Therefore, it is very important to ensure the consistent phenotype of each colony. CD Genomics developed a robust and sequencing-based platform to help scientists and biotechnology companies quickly and comprehensively characterize microbial strains.

NGS and long-read sequencing technologies offer a strong potential for microbial copy number analysis. Based on Illumina HiSeq/MiSeq, PacBio or Oxford nanopore sequencing platforms, we are able to determine the copy number of each transgene, thus providing quality control of your transgenic models. Long-read sequencing technologies is a powerful tool to cover complex repetitive regions. Further data analysis helps explain the relationship between transgene copy number and changes of phenotype or inconsistent performance of microbial strains. These information are crucial for understanding disease phenotype and drug efficacy analysis.

Copy number analysis workflow

Bioinformatics Analysis

Our bioinformatics analysis pipeline includes data quality control, copy number analysis and advanced analysis, which is flexible to your needs. Please feel free to contact us to discuss your project.

Bioinformatics Analysis Details
Data QC Read quality assessment, trimming and filtering
Copy Number Analysis Copy number analysis of targeted genes
Advanced Analysis Revelation of the corresponding outcomes resulted from changes of gene copy number

Sample requirement

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. Crosby L D, Criddle C S. Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques, 2003, 34(4): 790-802.

