Gencove Platform

The Gencove Platform is an integrated, end-to-end solution for genomic data generation, analysis, and management, designed for research and commercial teams working in human, plant, and animal genomics. By combining assay development, sequencing services, and cloud-based data analytics into a single cohesive platform, Gencove shortens the path from biological samples to actionable insights — enabling teams to predict genomic disease risk, discover and identify genetic traits, determine ancestry, establish parentage and relatedness, and drive trait improvement programs.

Gencove is built for organizations where genotyping at scale demands significant resources and expertise. The platform abstracts away infrastructure complexity, reduces operational overhead, and empowers data science teams to focus on results rather than pipeline management — all while ensuring users retain full ownership and control of their data.

Data Analytics and Management

• Gencove Explorer is a cloud-based tertiary genomics computing environment that enables scientists to organize, analyze, and visualize genomic datasets in one place.
• Shortcuts provide a built-in library of methods for common bioinformatics workflows, including merging, filtering, and annotating VCFs; calculating genotype discordance; performing genome-wide association studies (GWAS); and developing and calculating polygenic risk scores.
• Scalable compute clusters with private storage and a flexible, genomics-oriented interface with native integration to Gencove datasets.
• Consultative on-ramp projects with dedicated data science support from Gencove's expert team.
• Managed pipelines covering read alignment, imputation, variant calling, breed analysis, quality control, and sample metadata storage.
• Multiple access modes including web dashboard, command-line interface (CLI), and API, with third-party integrations such as AWS S3 buckets and Illumina BaseSpace.
• Sequencer-agnostic cloud connectivity allowing raw sequencing data transfer from any instrument, with automated demultiplexing of base calls into FASTQ files, sequencing run-level quality control, and automatic downstream analysis initiation.

Sequencing Services

• Low-pass whole genome sequencing (WGS) delivering the power of whole-genome analysis at array-comparable cost.
• High-coverage sequencing for comprehensive variant discovery.
• Innovative approaches such as low-pass WGS combined with capture, available across a range of species.
• Partner laboratories around the world accepting different sample types, maintaining relevant regulatory classifications, and handling both clinical and research samples.
• Deliverables ranging from raw FASTQs and comprehensive quality control statistics to fully processed variant calls, all delivered through the Gencove platform via web dashboard, CLI, or API.

Assay Development

• Custom probe design for targeted sequencing, providing enhanced coverage and higher-fidelity analysis at key loci.
• Cost-effective, high-throughput library preparation methods optimized by the Gencove lab team to keep costs down.
• Expert guidance on selecting the right library preparation kit and genotyping method for each specific project.

Platform Value Proposition

• Flexibility and customization at industrial scale through an automated, cohesive, and efficient data flow.
• Maximized data quality and analytical power relative to budget and project goals.
• Tools that enable teams to do more with less and bridge resource gaps.
• Continuous access to cutting-edge innovation through an expert team that tracks and navigates a rapidly evolving genomics landscape.
• Full data autonomy and ownership, ensuring privacy and control over data usage.

The Gencove Platform supports both research and applied genomics use cases across human health and agricultural sustainability, with deployment through a secure genomics cloud and integrations with widely used third-party data infrastructure.