Shallow Shotgun Sequencing

Comparison of cost and information content of several sequencing methods- Creative Biogene

Shallow shotgun sequencing is a novel sequencing method, which has the advantages of 16S sequencing and metagenomic sequencing simultaneously. Shallow shotgun sequencing combines more samples into a single sequencing run and uses a modified protocol with a lower volume of reagents to prepare the library.

Compared with amplicon sequencing, shallow shotgun sequencing provides a less biased representation of the microbial community and higher taxonomic resolution. However, it cannot replace full metagenomic research. The cost of shallow shotgun sequencing is slightly higher than that of amplicon sequencing and 16S sequencing but much lower than deep shotgun sequencing. It is an economical way to provide composition and function data.

Application & the Future of Shallow Shotgun Sequencing

With the continuous demand for cost-effective and high-quality microbiome data, shallow shotgun sequencing is going to be a widely used technique. The study of microorganisms in known environmental settings (such as the human intestine) has greatly benefited from the data generated by shallow shotgun sequencing.

With the future development of metagenome databases including novel microbial reference genomes, shallow shotgun sequencing will also facilitate the characterization of lesser-studied microbial environments. Finally, with the widespread application of multi-omics analysis, shallow shotgun sequencing will help gain more knowledge about the interaction of the microbiome with other omics, including metabolites, genomes, proteomics, etc.

Our Service Process

Application of shallow shotgun sequencing- Creative Biogene

Service Offering

Each shallow shotgun sequencing project includes,

  • Collect and process samples, then extract the DNA of the sample.
  • Preliminary quality control inspection on all samples, and the QC report returned to review.
  • Using our optimized approach to prepare library.
  • Sequencing starting at 2 million reads per sample.
  • Bioinformatics analysis report.

Our bioinformatics analysis covers a wide range including taxonomic assignment, microbial diversity analysis, function annotations, CAZy, CARD and pathogen prediction, etc.

Turnaround Time

In general, our turnaround time is 1-3 weeks depending on the size of your project.

Advantages of Our Services 

  • We have professional experts and we are in a leading position in microbial research.
  • Our well-established sequencing platform ensures the accuracy of the sequence.
  • We can combine the needs of customers, negotiate to determine the content of services
  • Short turnaround time and cost-effective.

Creative Biogene has excellent microbiology experts, well-established high-throughput sequencing platforms, and professional bioinformatics analysis to provide you with a one-stop service in shallow shotgun sequencing. Our services include sample collection, quality control, library construction, sequencing and analysis.

If you are interested in our services, please contact us for more details.


  1. Hillmann B, et al. (2018). "Evaluating the Information Content of Shallow Shotgun Metagenomics." MSystems 3.6.
For Research Use Only.
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