Full-length 18S / ITS Amplicon Sequencing Analysis

Full-length 18S / ITS Amplicon Sequencing Analysis

Online Inquiry

As a bioinformatics data analysis provider, CD Genomics offers comprehensive full-length 18S/ITS amplicon sequencing analysis services to help you explore the identification, diversity and taxonomy of fungi and other eukaryotes in complex communities. Our high-quality data analysis platform will be used to generate high-quality analysis results in a fast analysis cycle.

Introduction to 18S / ITS Amplicon Sequencing Analysis

16S/18S/Internal Transcribed Spacer (ITS) amplicon sequencing is widely used in microbial research because of its low cost, short cycle time, and low sample quality requirements. Among them, 18S and ITS sequencing is commonly used to identify fungi and other eukaryotes in environmental samples. Both methods use PCR to amplify DNA with specific primers, and the results are obtained after sequence processing, sequence analysis, and comparison. ITS sequencing is more focused on studying the intraspecific genetic diversity of fungi due to greater ITS variability, while 18S rRNA focuses on phylogenetic taxonomic studies of fungi. In recent years, scientists are developing full-length 18S/ITS amplicon sequencing methods based on PacBio and Oxford Nanopore sequencing technologies to identify a wider range of species and distinguish strains within species.

Fig. 1. Taxonomic classification of eukaryotic microbes using 18S amplicon sequencing.Fig. 1. Taxonomic classification of eukaryotic microbes using 18S amplicon sequencing. (Popovic A, et al, 2018)

Application Field

Our full-length 18S/ITS amplicon sequencing analysis can be used for but not limited to the following research:

Environmental microbiology: our full-length 18S/ITS amplicon sequencing analysis can help you characterize microbial communities in the environment and reveal their role in nutrient cycling, bioremediation, and overall ecosystem function.

Human microbiome research: our full-length 18S/ITS amplicon sequencing analysis can characterize microbial communities in different body parts, such as the gut, mouth, skin and reproductive tract. This analysis helps reveal the complex relationships between the human microbiome and various health conditions.

Agriculture and food safety: our full-length 18S/ITS amplicon sequencing analysis can be used to study microbial communities associated with crop health, soil fertility and plant-microbe interactions. It also helps to detect and monitor foodborne pathogens and spoilage microbes, ensuring food safety and quality throughout the production and distribution chain.

Biotechnology and pharmaceutical research: our full-length 18S/ITS amplicon sequencing analysis allows monitoring and characterizing these microbial communities, helping you to identify potential contaminants, optimize production conditions, and develop effective microbial control strategies.

CD Genomics Data Analysis Pipeline:

CD Genomics is a leading company in genomics and sequencing services, providing comprehensive and advanced bioinformatics analysis of full-length 18S/ITS amplicon sequencing data. Utilizing cutting-edge technology and expertise in the field, CD Genomics assists researchers and scientists in unraveling the complexity of microbial communities and their functions.

(1) Data pre-processing

Quality control and filtering of raw sequencing data obtained by sequencing full-length 18S/ITS amplicons to remove low-quality reads, adapter sequences and artifacts. CD Genomics employs stringent quality control measures to ensure reliable downstream analysis.

(2) Sequence alignment and clustering

CD Genomics performs sequence alignment using specialized algorithms and databases to map sequencing reads to reference databases, such as SILVA or UNITE for the 18S and ITS regions, respectively.

(3) Taxonomic analysis and diversity analysis

CD Genomics uses advanced bioinformatics tools to assign taxonomic identities to OTUs and generate taxonomic analysis histograms and abundance heat maps.

(4) Functional analysis:

CD Genomics can predict the abundance of functional pathways based on 16S copy number.

(5) Statistical analysis and visualization

CD Genomics uses various statistical methods and visualization techniques to reveal significant differences and relationships in the data. Multivariate statistical analyses are used to identify changes in microbial communities under different conditions or treatments. In addition, visualization methods such as principal component analysis (PCA) and ternary plots facilitate visualization and interpretation of complex microbial data sets.

Full-length 18S / ITS Amplicon Sequencing Analysis Content:

Species Annotation

Tag assembly

OTU clustering

Taxonomic analysis

Abundance heat map generation

Phylogenetic tree construction

Diversity Analysis

Alpha diversity

Beta diversity


Multivariate statistical analysis

How It Works

CD Genomics is a high-tech company specializing in multiomic data analysis. We provide services such as project design, data analysis, and database construction. With a focus on developing breakthrough products and services, we are a pioneer in the biotechnology industry, serving researchers and partners worldwide.

How It Works

CD Genomics provides valuable support and insight in areas such as these applications with its extensive experience and expertise in bioinformatics analysis of full-length 18S / ITS amplicon sequencing. We can help you gain a deeper understanding of the diversity, composition and function of your microbial community. From species annotation and diversity analysis to functional prediction and enterotype analysis, CD Genomics offers a comprehensive solution for unlocking the mysteries of the microbial world. If you are interested in our services, please contact us for more detailed information.


  1. Popovic A, Parkinson J. Characterization of eukaryotic microbiome using 18S amplicon sequencing[J]. Microbiome analysis: methods and protocols, 2018: 29-48.
* For Research Use Only. Not for use in diagnostic procedures.
Online Inquiry