Sr. Bioinformatics Engineer

Sr Bioinformatics Engineer (Hybrid in South San Francisco) 

Job Description

We're seeking a Senior Bioinformatics Engineer to join our team and help build robust, scalable infrastructure for processing and analyzing next-generation sequencing (NGS) data. This role bridges bioinformatics expertise with production engineering, focusing on creating reliable, high-performance computational pipelines. The ideal candidate will have strong experience in computational biology and bioinformatics method development, with the engineering skills necessary to translate research algorithms into production-ready solutions. They should have a proven track record of developing and implementing bioinformatics pipelines and be excited about tackling complex genomic data analysis challenges using cutting-edge sequencing technologies.

This role offers the opportunity to:

• Develop cutting-edge bioinformatics algorithms and pipelines


• Work with diverse sequencing technologies including Illumina NGS and ONT long-read platforms


• Solve complex computational biology challenges


• Build systems that advance genomic research and precision medicine

Key Responsibilities:

• Design and implement production-grade bioinformatics pipelines for processing NGS and ONT sequencing data, including genome assembly, variant calling, and structural variant detection


• Develop and optimize algorithms for long-read sequencing data analysis, including base calling, error correction, and assembly polishing


• Build reproducible computational workflows for multi-omics data integration and analysis using containerized solutions


• Implement robust quality control metrics, validation frameworks, and monitoring systems for sequencing data processing pipelines


• Develop and maintain CI/CD pipelines for bioinformatics tools and automated testing of genomic analysis workflows


• Collaborate with wet lab scientists to optimize sequencing protocols and troubleshoot data quality issues


• Architect and maintain scalable cloud infrastructure for deploying bioinformatics pipelines in production environments


• Develop custom bioinformatics software tools with proper version control, documentation, and testing practices


• Establish best practices for bioinformatics data management, pipeline deployment, and reproducible analysis at scale

What You’ll Bring to the Team:

Requirements:

• 5+ years experience in bioinformatics/computational biology with software engineering skills (MS/PhD preferred)


• Strong programming in Python, plus experience with Rust, Go, or C++ for performance applications


• Extensive experience with NGS and ONT sequencing analysis (alignment, variant calling, assembly, structural variants)


• Proficiency with bioinformatics tools (BWA, GATK, samtools, minimap2, flye) and workflow systems (Nextflow, Snakemake)


• Production software development experience including Git, unit testing, CI/CD, and containerization (Docker, Kubernetes)


• Cloud platform experience (AWS, GCP) and Linux/HPC environments


• Strong molecular biology and genomics knowledge


• Experience deploying bioinformatics pipelines in production environments (preferred)


• Background in synthetic biology, DNA design, or genomic library analysis

About Twist Bioscience

Twist Bioscience synthesizes genes from scratch, known as “writing” DNA. Just as children learn to both read and write, the next phase of development for the genomics revolution is the ability to write DNA.

At Twist Bioscience, we work in service of people who are changing the world for the better. In fields such as health care, agriculture, industrial chemicals and data storage, our unique silicon-based DNA Synthesis Platform provides precision at a scale that is otherwise unavailable to our customers.

Twist Bioscience Corporation is an Equal Opportunity Employer. Twist Bioscience Corporation provides equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability, genetic characteristics, or any other category protected by law.