Our experts transform innovative ideas into powerful web, SaaS, mobile, and specialized bioinformatics solutions.
Cloud Infrastructure & Data Engineering
- Enterprise Data Warehousing: Architecture and implementation of scalable genomic data warehouses using modern data platforms like Snowflake and Databricks, alongside native cloud services (AWS, Azure, GCP).
- Automated Ingestion & Data Management: Automated instrument data ingestion to cloud storage, centralized database parsing, and scalable facilities for exporting targeted genomic data (e.g., VCFs) for downstream analysis.
- Infrastructure as Code (IaC) & DevOps: Automated deployment and robust CI/CD pipelines utilizing industry standards such as Terraform, Octopus Deploy, GitHub Actions, GitLab CI, and advanced monitoring platforms like Datadog.
Automated Bioinformatics Pipelines
- Scalable Secondary Analysis: Development of robust, portable bioinformatics pipelines (e.g., Nextflow) deployed seamlessly across on-premises infrastructure and major cloud providers (AWS, Azure, GCP).
- Comprehensive Variant Calling: End-to-end pipelines for the mapping and calling of both small and structural variants.
- Automated QA & Visualization: Built-in quality assurance processes calculating key metrics, applying validation thresholds, and generating automated visualization plots to ensure run integrity.
Algorithm Development & Custom Integration
- Bespoke Algorithms: Development of proprietary algorithms, specialized workflows, and novel data analysis methods tailored to complex genomic challenges.
- Application & LIMS Integration: Custom plugin and extension development for primary user applications (such as Geneious, IGV, and other specialized software) and deep integration with Laboratory Information Management Systems (LIMS) to seamlessly enforce validation thresholds and connect external QC tools.
- Web Portals & APIs: Custom portals for client end-users or laboratory staff to interface with complex underlying pipelines.
Engineered an AWS/Snowflake data warehouse that automatically ingests instrument data and genotypes. The system features automated QA processes (such as sample sex and parentage verification) and enables seamless export of targeted VCFs, all managed via Terraform and continuously monitored with Datadog.
Developed and deployed Nextflow secondary analysis pipelines for both on-premise and AWS environments. These pipelines handle mapping and small/structural variant calling while generating comprehensive QA metrics and visualization plots.
Partnered with a client to develop extensive Nextflow secondary analysis pipelines incorporating bespoke algorithms. We actively participated in executing the rigorous validation studies required for their successful FDA CDx submission.
Streamlined a laboratory’s transgene validation workflow by developing custom plugins for the Geneious application. One plugin integrated various external QC tools directly into the UI, while another automatically collated metrics and applied strict thresholds to ensure runs met all validation criteria.