Whole genome discovery at the cost of genotyping

Gencove's low-pass sequencing platform is the most efficient solution for genomic discovery. Start sequencing and increase the power and scale of your genomic projects.

Starting at $50 per sample
  • Trusted by:

Our Technology

Gencove’s platform delivers the power of sequencing in a cost-efficient manner. Optimized library preparation and advanced imputation algorithms enable us to extract more information from every sequencing read.

Averaging across all known variation, low-pass sequencing outperforms genotyping arrays at common and rare variation. Since it does not have ascertainment biases, it’s the optimal technology for use across populations. At scale we can also identify new genetic variants that have never been seen before.

Learn more

Library preparation

Our library preparation method was developed specifically for low-pass sequencing. It is automated, resource efficient, and requires low amounts of input DNA. An optional capture step allows the addition of targeted genomic regions at high coverage.


We perform low-pass shotgun sequencing at 0.4 to 1x coverage using the latest Illumina technology. This results in an average of 50 times more measurements per genome than genotyping technologies.

Imputation & data analysis

We developed imputation algorithms for sequencing data to call variants across the whole genome with high accuracy (average imputation r2 over 0.9). Additionally, our standard data analysis includes ancestry and microbiome profiling of every sample.

Gencove low-pass imputation service

Upload your FASTQs


We work with researchers in biotech, pharma, biobanks, and academia, and we also power direct-to-consumer genomic tests and products.

Common use cases
  • Genetic association studies

  • Population genetics and ancestry profiling

  • Disease gene panels and polygenic risk profiling

  • Agricultural and animal genomics

  • Microbiome profiling

Select the product that best fits your needs

We offer our low-pass sequencing technology as an end-to-end solution, from sample preparation to analysis-ready data.

What our solutions include:

Move from genotyping arrays to sequencing


Illumina GSA


Data files: Imputed VCF file**, BAM file
Other results: Ancestry analysis, Microbiome, Novel variant discovery***


Increase your power to discover new genetic variation


Affymetrix Biobank
Illumina 2.5M


Data files: Imputed VCF file**, BAM file
Other results: Ancestry analysis, Microbiome, Novel variant discovery***

Plus Capture
Customized solution

Core or Discovery + targeted exon or SNP variant calls

Add custom content to target specific regions and/or variants while retaining competitive pricing.

+ targeted regions

Price based on a minimum batch of 94 samples
* Low-pass sequencing provides measurements at random sites in the genome that are covered by at least one sequencing read
** Imputation is based on the 1000 Genomes Phase 3 or HRC
*** Available for large cohorts
Pricing for more than 1000 samples

Need more?

If you have questions or custom requirements reach out to us

Contact Us

Asked Questions

We regularly process genomic DNA, saliva, and blood samples. Let us know if your samples are from other sources and we'll work with you to get them processed. Saliva samples can be collected using most commercial saliva collection kits or saliva collection swabs. Genomic DNA can be provided in standard 96-well plates or microcentrifuge tubes.

See here for detailed sample submission guidelines.

Results are returned within 6-8 weeks from the time samples arrive in our lab. Let us know if you have special requirements for turnaround time and we'll work with you to make sure your samples are done on time!

All customers get access to our data management website (https://app.gencove.com), where sample status can be tracked all the way from sample acceptance by our lab to delivery-ready data. In addition to the website, users can monitor sample status and automate data delivery by integrating with our REST API (https://docs.gencove.com).

Data can be accessed via the Gencove data management website or REST API. For downloading data in bulk, we recommend using the API or our command-line tool (https://docs.gencove.com/main/#the-gencove-cli).

Absolutely! You can use the API to track sample status and automate data delivery. Check out the docs here: https://docs.gencove.com

We regularly work with multiple sample collection kit manufacturers and logistics centers. Contact us and we can get you up and running.

We always use the latest Illumina sequencing machines. Depending on the specifics of your project, we'll use the NovaSeq, HiSeq X, or NextSeq.

Use Cases


Baker Institute - Genomic risk in celiac disease

Baker Institute is developing a genomic risk score that can help predict risk of celiac disease that is yet to manifest itself. Gencove’s low-pass sequencing will be used to establish the validity and utility of genomic risk approaches for identifying individuals at high risk.

Learn More

University of Michigan -    PSID

The Panel Study of Income Dynamics (PSID) is the world’s longest running household panel survey. Gencove’s low-pass sequencing is being used to add genomic information to the study with the aim of fully understanding the interplay of genetics and environment over the life course of the participants.

Learn More
Animal genomics

Broad Institute - Darwin’s Dogs

Darwin's Dogs is a crowd-sourced genomics project studying how the dog genome has changed through history. Using low-pass sequencing, researchers are studying how genetics shapes behaviour, and psychiatric and neurological diseases in both dogs and people.

Learn More
Conservation genomics

Stanford University - Conservation Genomics

The program is developing tools for the next generation of conservation scientists. By using low-pass genome sequencing, they are investigating the population genomics of endangered mammals like rhinos, tigers, and lions. In addition, they are sequencing sanctuary and captive animals in order to understand how the illegal wildlife trade impacts wild populations and their cosmopolitan trade routes.

Learn More
Whole genome sequencing complement

University of Utah - Gene discovery in diabetes

Researchers are applying a novel and innovative approach to accelerate gene discovery in diabetic kidney disease that integrates big data from the Utah Population Database. Deep whole-genome sequencing on select members of these pedigrees is being combined with Gencove's low-pass sequencing data on additional individuals from high-risk families.

Learn More

Learn More
Show More

About Us

We are a group of scientists, engineers, and entrepreneurs who are building a future where genome sequencing is accessible and interpretable.

Joe Pickrell
CEO & Co-founder

Joe is a statistical geneticist who has published scientific papers in the most selective scientific journals like Nature, Science, Nature Genetics, and PNAS. Prior to founding Gencove, he was a professor at New York Genome Center and Columbia University, and he holds a PhD in Human Genetics from the University of Chicago.

Tomaz Berisa
CTO & Co-founder

Tomaz spends his time at the intersection of genomics and computer science, and is responsible for tech at Gencove. Prior to founding Gencove, he was a data scientist at the New York Genome Center. He holds a PhD in Electrical Engineering from the University of Zagreb.

Read the full story