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Viral Metagenomic Sequencing

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CD Genomics is committed to providing unprecedented amounts of sequence data permitting rapid and innovative analytical approaches with cost-effective solutions.

Viruses are the most abundant biological entities in the world which outnumber microbial cells 10:1 in most environments. The viral community is also named as virome. Viral metagenomics (or viromics) can provide insights into the composition and structure of environmental viral communities, it has promising applications including virus discovery and viral pathogen identification associated with horticulture, veterinary medicine and human health, which shows significant advantages over traditional methods, especially for the difficult-to-diagnose cases.

Given the fact that viral DNA only represents 0.1% of the total DNA in a microbial community, the basic steps involved in viral metagenomics include isolation and purification of viral particles (VPs) by size filtration or density-based centrifugation, sequence-independent amplification of viral nucleic acid, sequencing and finally use of bioinformatics tools to analyze the diversity, taxonomy, and function. The workflow for the viral metagenomic sequencing is demonstrated in Figure 1.

Workflow of viral metagenomic sequencing Figure 1. Workflow of viral metagenomic sequencing.

Data Analysis

A common output data analysis pipeline is illuminated in Figure 2. Firstly, the host and bacterial genomic sequences are filtered, then the remaining reads are mapped to reference viral genome, the downstream gene prediction, gene function annotation, gene variation discovery programs are carried out. 

A typical pipeline for viral metagenomics data analysis. Adapted from  Rampelli <em>et al.</em>, 2016 Figure 2. A typical pipeline for viral metagenomics data analysis. Adapted from Rampelli et al., 2016.

Recommend Sequencing Platform and Sequencing Depth

  • HiSeq PE150 and 2Gb raw data per sample

In the process of viral metagenomics service, we can help in the experimental design at the very beginning of your project, by guiding to choose suited sequencing platform, appropriate software tools, and analysis methodologies to accommodate your circumstances, and maintain referring to the most up-to-date virus databases. If you have additional requirements or questions, do not hesitate to contact us, our Ph.D.-level specialists would like to help you solving your questions.


  1. Rampelli, S. et al. ViromeScan: a new tool for metagenomic viral community profiling. BMC Genomics. 2016, (17):165.
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