Bioinformatics Pipeline Engineer - NGS & Linux

Mount Sinai Morningside; New York (NY); On-site; USD 65,000 - 91,000; Full time

Job summary

Mount Sinai Morningside in New York seeks a Bioinformatician to implement, validate, optimize, and maintain robust workflows in a Linux environment. You will build and refine NGS pipelines covering alignment, QC metrics, annotation, and downstream analysis, with an emphasis on reproducibility and documentation.

You will collaborate with wet-lab, QA, clinical operations, and product teams to ensure pipelines meet scientific and regulatory standards, while maintaining version control, release

Qualifications

• Bachelor's degree in biological sciences, bioinformatics, computer science, or statistics; MS preferred.
• At least 3 years' experience; 2+ years software development in a Linux environment preferred.
• Experience programming in Python, R, or Bash.
• Solid understanding of NGS technologies and analytical methods.
• Proficiency with workflow management systems such as Nextflow, Snakemake, or WDL/Cromwell.
• Strong Linux system administration knowledge.
• Experience implementing and validating bioinformatics tools in regulated or semi-regulated environments.

Responsibilities

• Implement NGS bioinformatics pipelines, including annotation, QC workflows, and downstream analytical components
• Own end-to-end validation of implemented pipelines, ensuring they meet scientific and regulatory requirements
• Execute software verification and validation (SV&V) protocols and maintain thorough documentation of all results
• Evaluate new tools, algorithms, and software for integration into analytical workflows
• Troubleshoot pipeline failures and drive root-cause analyses
• Ensure reproducibility, scalability, and robustness of computational workflows
• Partner with wet-lab teams, quality assurance, clinical operations, and product management to align implementation and validation objectives with project timelines and business needs
• Maintain detailed records of implementation, validation activities, version control, and release notes
• Prepare documentation in support of internal quality audits
• Other related duties as assigned.

Skills

Python

R

Bash

Linux

Nextflow

Snakemake

WDL/Cromwell

Education

Bachelor's degree in Biological Sciences, Bioinformatics, Computer Sciences, Statistics or related discipline; MS preferred

Tools

Nextflow

Snakemake

WDL/Cromwell

Job description

Mount Sinai Morningside in New York seeks a Bioinformatician to implement, validate, optimize, and maintain robust workflows in a Linux environment. You will build and refine NGS pipelines covering alignment, QC metrics, annotation, and downstream analysis, with an emphasis on reproducibility and documentation.

You will collaborate with wet-lab, QA, clinical operations, and product teams to ensure pipelines meet scientific and regulatory standards, while maintaining version control, release