Senior Bioinformatics Engineer

Clovertex; Hyderabad; On-site; INR 1,800,000 - 2,800,000; Full time

Job summary

Clovertex is seeking a Senior Bioinformatics Engineer to design, develop, automate, and optimize genomics workflows for production-ready cloud-scale solutions. You will work with scientists, cloud engineers, and clients to translate complex bioinformatics requirements into scalable software.

The role emphasizes Python development, NGS data analysis, and experience with workflow engines like Nextflow, WDL, or Snakemake, along with Linux and containerization expertise.

Qualifications

• Master's or PhD in Bioinformatics, Computational Biology, Biotechnology, Genomics, or related field.
• 3–5 years of industry experience in Bioinformatics or Scientific Computing.
• Strong programming skills in Python.
• Hands-on experience with NGS data analysis and genomics workflows.
• Experience with Nextflow, WDL, Snakemake, Cromwell, or similar workflow engines.
• Strong understanding of Linux environments and shell scripting.

Responsibilities

• Design, develop, and maintain bioinformatics workflows for NGS, genomics, and multi-omics applications.
• Build and optimize scalable pipelines using Nextflow, WDL, Snakemake, Cromwell, or similar workflow frameworks.
• Develop production-grade software and automation solutions using Python.
• Work with large-scale genomics datasets and scientific applications in cloud environments.
• Containerize and deploy scientific applications using Docker and related technologies.
• Collaborate with scientists, bioinformaticians, architects, and client stakeholders to translate scientific requirements into technical solutions.
• Participate in solution design discussions, customer meetings, technical workshops, and project planning activities.
• Work closely with cloud, data, and AI engineering teams by providing strong bioinformatics domain expertise and guidance for scientific solution development.
• Contribute to software engineering best practices including version control, testing, CI/CD, documentation, and code reviews.

Skills

Python

Bioinformatics

NGS data analysis

Linux

Shell scripting

Education

Master's/PhD in Bioinformatics/Genomics

Tools

Nextflow

WDL

Snakemake

Cromwell

Docker

Job description

We work with leading global pharmaceutical, biotechnology, and healthcare organizations, primarily across the US and Europe, helping them build, modernize, and optimize scientific and bioinformatics platforms. As a Life Sciences-focused engineering organization and a close AWS Life Sciences Partner, we specialize in delivering cloud-native bioinformatics, genomics, and scientific computing solutions.

Strong communication skills and the ability to interact directly with global clients are critical for this role.

About the Role

We are looking for a Senior Bioinformatics Engineer with strong bioinformatics and software engineering expertise to design, develop, automate, and optimize genomics and multi-omics workflows. This is an engineering-focused role where you will work closely with scientists, cloud engineers, architects, and customers to build scalable and production-ready bioinformatics solutions.

Key Responsibilities

• Design, develop, and maintain bioinformatics workflows for NGS, genomics, and multi-omics applications.
• Build and optimize scalable pipelines using Nextflow, WDL, Snakemake, Cromwell, or similar workflow frameworks.
• Develop production-grade software and automation solutions using Python.
• Work with large-scale genomics datasets and scientific applications in cloud environments.
• Containerize and deploy scientific applications using Docker and related technologies.
• Collaborate with scientists, bioinformaticians, architects, and client stakeholders to translate scientific requirements into technical solutions.
• Participate in solution design discussions, customer meetings, technical workshops, and project planning activities.
• Work closely with cloud, data, and AI engineering teams by providing strong bioinformatics domain expertise and guidance for scientific solution development.
• Contribute to software engineering best practices including version control, testing, CI/CD, documentation, and code reviews.

Required Skills

• Master's/PhD degree in Bioinformatics, Computational Biology, Biotechnology, Genomics, or a related field.
• 3–5 years of industry experience in Bioinformatics or Scientific Computing.
• Strong programming skills in Python.
• Hands-on experience with NGS data analysis and genomics workflows.
• Experience with Nextflow, WDL, Snakemake, Cromwell, or similar workflow engines.
• Strong understanding of Linux environments and shell scripting.
• Experience working with cloud-native genomics platforms and AWS services such as S3, AWS Batch, AWS HealthOmics, ECR, CloudWatch, IAM, and related services used for scientific workloads.
• Good understanding of genomics workflow optimization, workflow orchestration, and scalable compute environments.
• Excellent written and verbal communication skills.
• Ability to work directly with international clients and participate in technical discussions independently.

Preferred Skills

• Experience with RNA-Seq, WGS, WES, Single Cell, Proteomics, or Multi-omics workflows.
• Experience with Docker and containerized bioinformatics applications.
• Exposure to HPC environments, SLURM, or scientific computing platforms.
• AWS certifications or practical experience working on AWS-based genomics solutions.
• Understanding of modern data platforms, AI-driven scientific solutions, and emerging technologies within life sciences.
• Exposure to customer-facing engagements, technical solutioning, or presales activities.

What We Look For

• Strong engineering mindset with a passion for bioinformatics and scientific computing.
• Excellent communication and client-facing skills.
• Ability to learn quickly and adapt to new technologies and domains.
• Strong ownership, problem-solving, and collaboration skills.
• Interest in building scalable, production-grade scientific solutions for leading global pharmaceutical and biotechnology organizations.