DeepSeq is our deep shotgun metagenomic sequencing approach that generates truly big data. Unlock the signatures in your microbiome samples with DeepSeq.

Big Data Sequencing

DeepSeq is big data.

Starting at 20 million reads per sample, DeepSeq gives you the most information possible for your microbiome samples.

If you need to know more about rare members of the microbiome, or if you’re on the hunt for novel strains, DeepSeq is for you.

Each project includes species level taxonomic profiling and functional profiling of biological pathways as well as strain coverage information.

DeepSeq data can be used to assemble and bin metagenomic species. DeepSeq also provides functional data from low-biomass samples that are not suited for BoosterShot™.

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

Sample Types Suited for DeepSeq

Samples with high biomass generate the best microbiome data in DeepSeq.

Because shotgun metagenomic 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 utilizing 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.

Gain Novel Insights

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

Pairing DeepSeq 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 can help minimize pain points. Pairing DeepSeq with custom downstream analysis is our speciality.

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

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

DeepSeq Basics


Starts at $249 per sample.

Minimum order.

88 samples for 5-week turnaround, 24 samples for 8-week turnaround.


Adaptor-removed and filtered sequencing data (fastq), trimmed and combined sequences file (fasta), taxonomy and function tables, strain coverage tables, quality-control dashboard, and Core Analysis report. Review example report.


DeepSeq uses a CLIA approved workflow and is performed in a CLIA-certified laboratory.

DeepSeq includes:

  • Initial quality control check on all samples
  • QC report returned for review
  • Amplification and library preparation using our optimized approach
  • Sequencing starting at 20 million reads per sample
  • 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

DeepSeq sequencing starts at $249 a sample.

To ensure high-quality data, we require a minimum of 24 samples per project.

Standard turnaround time for a DeepSeq project is five weeks from DNA generation.

Large projects beyond 1,000 samples may require additional time. Contact us ​with questions.

To ensure your DeepSeq samples return the best data, we recommend performing your DNA extraction through CoreBiome.

Input DNA quality and quantity can have dramatic impacts on the microbial profile generated for your samples.

By allowing the experts at CoreBiome to extract and prepare your DNA, we can ensure the best quality library preparations for amplicon sequencing.

CoreBiome accepts primary samples, such as swabs, fecal samples, and soil, as well as pre-extracted DNA.

For more information regarding sample preparation and shipment, check out our sample guidelines.

All we need to know are some quick details regarding the types of samples you have, how many, and how they are stored.

From there, our team of experts can recommend the best approach for generating your microbiome data and discoveries.

Request a quote or contact us with questions.

For research and detection purposes only.

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