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Shotgun Metagenomics Data Analysis

Shotgun Metagenomics Data Analysis

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As one of the providers of shotgun metagenomics data analysis, CD Genomics uses bioinformatics to help you analyze metagenomics to quantify community structure and diversity, assemble new genomes, identify new taxa and genes, and determine the metabolic pathways encoded in the community. Our high-quality data analysis platform will be used to generate high-quality analysis results in a fast analysis cycle.

Research Advances in Shotgun Metagenomics Data Analysis

Microbial communities consisting of bacteria, fungus, viruses, and single-celled eukaryotes play a critical role in the environment and human health. However, the complexity and diversity of these communities make culturing and classifying their members challenging using traditional laboratory techniques. To overcome these limitations, shotgun metagenomics sequencing has emerged as a relatively new and powerful environmental sequencing method that can provide insight into the biodiversity and function of communities. However, analysis of shotgun metagenomics sequencing is complicated by the complex structure of the data. Fortunately, new tools and data resources have been developed to circumvent these complexities and allow researchers to determine which microbes are present in the community and how they function.

Fig. 1. Shotgun metagenomic sequencing data analysis pipeline.Fig. 1. Shotgun metagenomic sequencing data analysis pipeline. (Gao B, et al, 2021)

Application Field

Our shotgun metagenomics data analysis can be used for but not limited to the following research:

Environmental research: our shotgun metagenomics data analysis allows researchers to explore the diversity and functional potential of microbes in different environmental ecological niches. By studying microbial communities in soil, water, and other ecosystems, our researchers can gain insight into nutrient cycling, bioremediation processes, and the effects of environmental change. CD Genomics' shotgun metagenomics service facilitates environmental monitoring, identification of new microbial species, and discovery of potential biotechnology applications.

Human microbiome research: Our shotgun metagenomics allows characterization of the human microbiome, helping researchers understand its composition, dynamics and functional contributions. CD Genomics' expertise in the analysis of shotgun metagenomics data allows us to help you uncover the intricate interactions between the human microbiome and host health.

Biotechnology innovation: our shotgun metagenomics data analysis can help harness the power of microbes. By identifying novel genes, enzymes, and metabolic pathways from complex microbial communities, we can help you can discover new therapeutic targets, develop innovative drug discovery strategies, and design microbial factories to sustainably produce valuable compounds.

CD Genomics Data Analysis Pipeline:

CD Genomics offers a comprehensive service for shotgun metagenomics data analysis, allowing the elucidation of taxonomic composition, functional potential, and even the recovery of entire genomic sequences from microbial communities. Our services cover the entire workflow of shotgun metagenomics data analysis from pre-processing to data analysis.

(1) Data pre-processing and quality control

CD Genomics performs stringent quality control checks to remove low-quality reads, trim adapter sequences, and filter out contaminants. This step ensures that only high-quality, reliable data is used for downstream analysis.

(2) Taxonomic analysis of the microbiome

CD Genomics assigns taxonomy to sequencing reads using a computational pipeline and reference database. By comparing the mapped reads to a comprehensive set of microbial genomes, the relative abundance and diversity of different taxa in a sample can be determined. This analysis provides insights into the taxonomic composition and structure of the microbial community.

(3) Functional analysis of the microbiome

To reveal the functional potential of microbial communities, CD Genomics performs functional annotation of metagenomics data. This involves predicting and annotating genes, functional pathways and biological processes encoded in sequenced reads. Various bioinformatics tools and databases are used to annotate genes based on their homology to known functional elements.

(4) Sequence analysis of genomic features of the microbiome

CD Genomics uses advanced alignment algorithms or ab initio assembly methods to match sequencing reads to known genomes or to reconstruct the genome of individual microbial species within a community. This step allows for taxonomic analysis and identification of functional elements in metagenomics data.

(5) Post-processing statistical and biological analysis

CD Genomics uses advanced statistical analysis methods, data visualization techniques and comparative genomics approaches to identify significant patterns, potential interactions and functional features in microbial communities. Results are presented in a comprehensive report or visualization format to facilitate data interpretation and further exploration.

(6) Validation

CD Genomics provides comprehensive follow-up support for researchers, including in-depth consultation, interpretation of analysis results, and assistance with further data exploration or downstream analysis.

Shotgun Metagenomics Data Analysis Content:

Microbial Taxonomic Composition Analysis CD Genomics uses a sophisticated computational pipeline to analyze the taxonomic composition of microbial communities based on shotgunmetagenomics data.
Microbial Functional Potential Analysis CD Genomics utilizes comprehensive databases and cutting-edge algorithms to annotate genes and predict functional pathways encoded in metagenomics datasets.
Microbial Whole Genome Sequencing and Assembly CD Genomics provides the ability to recover entire genome sequences from shotgunmetagenomics data. By leveraging advanced assembly algorithms and data integration strategies, CD Genomics can reconstruct the genomes of individual microbial species present in a community.

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 is a leading provider of shotgun metagenomics data analysis services with its cutting-edge technology, expert team, customized solutions, and commitment to data security. Through our comprehensive analysis process, researchers can unravel the complexity of microbial ecosystems, paving the way for groundbreaking discoveries and advances in a variety of scientific fields. If you are interested in our services, please contact us for more detailed information.


  1. Gao B, Chi L, Zhu Y, et al. An introduction to next generation sequencing bioinformatic analysis in gut microbiome studies[J]. Biomolecules, 2021, 11(4): 530.
* For Research Use Only. Not for use in diagnostic procedures.
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