DEEPSEQ™Deep Shotgun Metagenomic Sequencing

DeepSeq is our highly-accurate deep shotgun sequencing approach that generates truly big data and lets you uncover the signatures in your microbiome samples.

Our deep shotgun sequencing approach allows you to characterize the most minor members of a microbiome, down to just 0.01% of a microbial community. 

Every DeepSeq project includes a Core Analysis™ Report which provides fully annotated data tables, interactive visualizations and all the raw data delivered through our customer portal.

Get Big Data

DeepSeq is big data.

Our deep shotgun sequencing approach gives you the most information possible for your microbiome samples. Sequencing depth is tailored to your research goals and each project includes species level taxonomic profiling and functional profiling of biological pathways as well as strain coverage information.

Review an example of a Core Analysis report with taxonomy and function tables, a quality-control dashboard, and interactive profile plots similar to the deep shotgun sequencing data return.

Gain Novel Insights

With​ DeepSeq you can unlock all the information in your microbiome samples.

Pairing our approach with closed-reference alignment allows you to characterize the most minor members of a microbiome, down to just 0.01% of the community. This alignment approach can also be used for other kingdoms, such as viruses, fungi, and archaea.

Going deep also allows you to assemble, bin, and determine metagenomic species within your samples. 

This technique was recently used by Pasolli et al1 to discover over 15,000 novel genomes from 9,428 samples.

Although assembly and binning can be difficult, our CorePlus Analysis option will help minimize pain points. Pairing deep shotgun sequencing with custom downstream analysis is our specialty.

Talk to our bioinformaticians about how you can pair DeepSeq with CorePlus Analysis to


Contact us to find out how we can help enrich your studies.

[1] Pasolli, et al. 2019. Cell. 2019. 176, 649-662.

Sample Types Suited for Deep Shotgun Metagenomic Sequencing

Samples with high biomass generate the best microbiome data with deep shotgun  sequencing.

Because shotgun sequencing generates data for all DNA in a sample, samples with high host-contamination (>50% of DNA) will result in sequencing data with many host genome reads. Host contamination should not be a deterrent from using our DeepSeq technology, as host contamination can be overcome with additional sequencing depth. ​

Contact one of our microbiome scientists to find the right balance of depth and data for your project.

DeepSeq Deep Shotgun Sequencing Basics

Suggested Sample Types

Once we fine tune the target sequencing depth for your research goals, almost any sample type can benefit from deep sequencing.  For more information regarding sample preparation and shipment, check out our sample guidelines.

We have experience working with a wide array of samples types, some of the most common types that are suitable for deep shotgun sequencing are listed below. Contact us if your sample of interest is not represented here.

  • Primary Samples (ex. stool, saliva, biopsies, urine, GI contents)
  • Mixed microbial communities and microbial consortia
  • Swabs (ex. skin, nasal, vaginal, oral, rectal, environmental/surface)
  • Soil and other environmental samples
  • Pre-extracted DNA (for the best data quality, please allow us to perform the extraction)


Your project includes:

  • Initial quality control check on all samples
  • QC report returned for review
  • Amplification and library preparation using our optimized approach
  • Whole Genome Sequencing at a depth tailored to your research goals
  • Core Analysis Report
    • Strain-level and species-level taxonomic assignments via fully optimal gapped
      DNA sequence alignment to a curated reference database
    • Direct functional profiling via alignment to a curated reference database, reported as KEGG orthology groups, modules, and pathways
    • Strain coverage tables
    • Sequencing quality-control dashboard
    • Interactive visualizations that leverage your sample metadata
    • Fastqs: adaptor-trimmed and quality-filtered sequencing data
    • Fasta: trimmed and combined DNA sequences in QIIME-ready format

Review example report.

Want to get the most out of your DeepSeq data? Talk to one of our bioinformaticians about our fully customizable CorePlus Analysis.

Turnaround Times:

Project turnaround times can be adjusted to meet your needs.

In general, our turnaround times are 4-6 weeks depending on the size of your project.


Diversigen provides services and generates data for research purposes only.  Not all services are available in all regions.