Senior Scientist - NGS Bioinformatics

Amgen Technology; Hyderabad; On-site; INR 4,000,000 - 7,000,000; Full time

Job summary

Amgen Technology in Hyderabad, India, is seeking a Senior Scientist in NGS Bioinformatics (Data Standardization Platform Integration) to standardize, validate, and scale NGS data workflows. You will ensure reproducible pipelines and enable integration into existing data systems for analytics and platform use.

Working with bioinformatics scientists, data scientists, software engineers, and lab scientists, you will help make sequencing data well-structured, consistent, and ready for reuse across

Qualifications

• PhD required or Master’s with 8+ years directly related experience.
• Bachelor’s with 10+ years directly related experience.
• Experience standardizing, validating, and scaling NGS workflows.

Responsibilities

• Standardize, validate, and optimize NGS workflows for reproducible and scalable sequencing analysis.
• Improve pipeline runtime, memory efficiency, and output consistency.
• Develop NGS data models, metadata standards, and structured output formats.
• Collaborate with scientists and engineers to integrate sequencing data into enterprise platforms.
• Support validation and reproducibility practices for long-term operations.

Skills

NGS workflows

Workflow optimization

LIMS data capture

Containerization

Nextflow

Snakemake

Enterprise data platforms

Cloud/HPC environments

Education

PhD

Masters + 8+ years

Bachelor's + 10+ years

Tools

Nextflow

Snakemake

LIMS

Docker/Kubernetes

Job description

Job Summary

Senior Scientist - NGS Bioinformatics (Data Standardization Platform Integration)

The Bioinformatician NGS (Data Standardization Platform Integration) will support Large Molecule Discovery by standardizing, validating, and scaling NGS data workflows so sequencing outputs can be reliably reused across research programs and enterprise platforms. This role will focus on making NGS pipelines reproducible, efficient, and ready for integration into existing data systems and downstream analytics.

Working closely with bioinformatics principal scientists, data scientists, software engineers, and laboratory scientists, this individual will help ensure sequencing data is well structured, consistent, and suitable for broader use in analytics, machine learning, and platform-enabled research. The role combines workflow optimization, data standardization, and platform integration, and is well suited for someone who enjoys building robust computational systems that improve scale, consistency, and reuse.

In this role, your core responsibilities include:

• Standardize, validate, and optimize NGS workflows to support reproducible and scalable sequencing analysis across research programs and data analysis pipelines.
• Improve pipeline performance, including runtime, memory efficiency, operational reliability, and consistency of outputs.
• Support development of NGS data models, metadata standards, and structured output formats to ensure sequencing information is captured and stored appropriately for downstream use in the database/CDL and broader informatics ecosystem.
• Collaborate closely with bioinformatics scientists, data scientists, software engineers, and laboratory scientists to align workflow requirements and integration sequencing data into enterprise platforms for analytics, reporting, and downstream reuse.
• Support validation, testing, and reproducibility practices that help ensure sequencing workflows are reliable, traceable, and suitable for long-term operational use.

Qualifications

Basic Qualifications:

• Doctorate degree PhD
• Or Masters degree with 8+ years of directly related experience
• Or Bachelors degree and 10+ years of directly related experience

Preferred Qualifications:

• PhD with 5+ years of experience standardizing, validating, and scaling NGS workflows for reproducible use across research programs or enterprise environments.
• Strong background in workflow performance optimization, including runtime, memory efficiency, and operational stability.
• Familiarity with workflow management and orchestration tools such as Nextflow or Snakemake.
• Experience with structured NGS data capture in LIMS for downstream analytics and platform use.
• Experience integrating bioinformatics outputs into enterprise data platforms and structured repositories with an emphasis on supporting data governance, traceability, and reproducibility for scientific datasets.
• Experience working closely with data scientists to ensure scientific data is modeled, saved, and organized correctly for downstream use.
• Familiarity with containerization and cloud- or HPC-based execution environments.