Lead Bioinformatics Engineer
Location: Hyderabad (Hybrid)
Employment Type: Full-Time
Experience: 6–10 Years
About Clovertex
At the intersection of science and technology, Clovertex is a Life Sciences Systems Integrator specializing in architecting, building, automating, and managing scientific applications, bioinformatics workflows, data platforms, AI solutions, and cloud-native infrastructures for leading pharmaceutical, biotechnology, diagnostics, and healthcare organizations.
As an AWS Advanced Tier Partner, we combine deep scientific expertise with modern engineering practices across Bioinformatics, Cloud Computing, Data Engineering, Scientific Computing, Artificial Intelligence, Generative AI, and Agentic AI. We work with Top 50 Pharmaceutical Companies, CROs, and Clinical Genomics Organizations using AWS and Bioinformatics best practices to deliver scalable, production-grade solutions.
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Position Overview
We are seeking a highly motivated and experienced Lead Bioinformatics Engineer to drive the design, development, deployment, and support of Bioinformatics, Data Engineering, and AI-enabled solutions for global Life Sciences and Healthcare clients.
This role combines scientific expertise with modern engineering practices and requires hands-on experience across NGS analytics, workflow engineering, cloud-native bioinformatics platforms, and technical leadership. You will work closely with scientists, bioinformaticians, cloud engineers, data engineers, AI engineers, and client stakeholders to build scalable, reproducible, and production-grade solutions.
The ideal candidate is passionate about applying engineering excellence to scientific challenges and enjoys working at the intersection of Bioinformatics, Cloud, Data Engineering, and AI.
Key Responsibilities
- Lead bioinformatics projects involving genomics, transcriptomics, multi-omics, and precision medicine initiatives.
- Design, develop, optimize, and maintain bioinformatics pipelines and workflows.
- Analyze and interpret NGS datasets including WGS, WES, RNA-Seq, scRNA-Seq, and other omics data.
- Architect scalable workflow solutions using modern workflow orchestration platforms.
- Work closely with clients to gather requirements, propose solutions, and provide technical leadership.
- Mentor and guide junior bioinformaticians and engineers.
- Establish best practices for workflow development, validation, testing, documentation, and deployment.
- Collaborate with cloud, DevOps, and data engineering teams for production deployments.
- Participate in technical design reviews, estimations, solution architecture discussions, and presales activities.
- Ensure quality, reproducibility, scalability, and operational excellence across projects.
- Support cloud migration, workflow modernization, and scientific platform engineering initiatives.
- Contribute to AI-enabled scientific workflows, automation, and innovation initiatives.
Required Technical Skills
Bioinformatics & Genomics
- Strong understanding of genomics, transcriptomics, and molecular biology concepts.
- Hands-on experience with NGS data analysis.
- Experience working with:
- Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), RNA-Seq, Single Cell RNA-Seq (preferred), Variant Analysis and Annotation, Multi-omics data integration (preferred)
Workflow Engineering
- Strong expertise in one or more workflow platforms:
- Nextflow, WDL/Cromwell, Snakemake, CWL
- Experience developing production-grade and scalable workflows.
- Experience optimizing workflow performance, scalability, and reproducibility.
Programming
- Strong proficiency in: Python, R, Bash/Shell Scripting
- Experience with software engineering best practices, Git, code reviews, CI/CD, and testing frameworks.
Cloud & Infrastructure
- Hands-on experience with AWS-based bioinformatics environments.
- Familiarity with services such as: AWS Batch, S3, EC2, Lambda, ECR, Step Functions, AWS HealthOmics (preferred)
- Experience with Docker and containerized workflow deployments.
- Familiarity with cloud-native scientific computing environments.
Preferred Skills (Good to Have)
- Exposure to Data Engineering concepts and platforms.
- Experience working with data lakes, metadata-driven architectures, ETL pipelines, and large-scale scientific datasets.
- Familiarity with AI/ML applications in Life Sciences.
- Exposure to Generative AI, LLMs, Agentic AI, RAG, Knowledge Graphs, or AI-assisted scientific workflows.
- Knowledge of HPC environments, SLURM, PBS, or scientific computing platforms.
- Experience with Kubernetes, Terraform, Infrastructure-as-Code, or DevOps practices.
- Experience supporting regulated healthcare, pharmaceutical, diagnostics, or genomics environments.
- Experience with AWS HealthOmics or cloud migration of scientific workflows.
Leadership & Soft Skills
- Strong stakeholder management and communication skills.
- Ability to lead client-facing technical discussions.
- Experience mentoring and managing small to medium-sized technical teams.
- Strong analytical and problem-solving mindset.
- Ability to work independently in a fast-paced and dynamic environment.
- Excellent written and verbal communication skills.
- Strong collaboration skills across scientific and engineering teams.
Education
- Master's or PhD in Bioinformatics, Computational Biology, Biotechnology, Genomics, Computer Science, Data Science, or a related field.
- Exceptional candidates with relevant industry experience may also be considered.
What Success Looks Like
- Delivering scalable and production-ready bioinformatics workflows.
- Leading technical discussions with clients and internal stakeholders.
- Driving cloud-native adoption and workflow modernization initiatives.
- Mentoring junior engineers and establishing engineering best practices.
- Contributing to AI, Data Engineering, and Scientific Computing initiatives.
- Supporting solution architecture, estimation, presales, and technical strategy activities.
If you are passionate about Bioinformatics, Cloud Computing, Data Engineering, and AI, and want to work on cutting-edge scientific solutions for leading healthcare and life sciences organizations, we'd love to hear from you.