Sr Software Engineer, Bioinformatics Pipelines

POSITION SUMMARY

The Bioinformatics Pipelines Engineering team at Natera builds and maintains analytical bioinformatics pipelines to reliably translate raw genomic data into clinically actionable insights for a global patient population. We optimize development velocity across R&D and Engineering. We deliver high quality, reliable, compliant production bioinformatics pipelines and associated infrastructure with global reach and scale. And we provide Natera diagnostic tests with the “secret sauce” needed for commercial success. 

The Pipelines Engineering team seeks a software / bioinformatics engineer to develop new and refine existing bioinformatics pipelines with global impact and tremendous scale. In this role you will work as an integral part of a globally distributed development team collaborating closely with R&D to develop production algorithms from statistical models and prototypes and to create data analysis tools supporting research efforts. You will also work closely with stakeholders to define product requirements and translate requirements to corresponding software designs.

PRIMARY RESPONSIBILITIES

• Implement new and enhance existing functionality in our portfolio of pipelines supporting Natera’s business

• Lead the end to end delivery of functionality, from requirements to deployment

• Process large numerical datasets efficiently

• Support and extend our next generation sequencing framework

• Troubleshoot and resolve defects, craft reliable unit tests, perform code reviews and root cause analysis

• Continue improving processes and procedures and evangelizing best practices

• Understand and be compliant with regulatory, security and data privacy requirements 

QUALIFICATIONS:

• BS Computer Science, Bioinformatics, Information Systems, etc. MS preferred.

• Data Structures / Algorithms Coursework

KNOWLEDGE, SKILLS AND ABILITIES

• Containerization: Docker (preferred), Singularity

• Orchestration: DNAnexus (preferred), SevenBridges, Azure / AWS Batch, Cromwell, Kubernetes, Toil, miniWDL, AWS Omics

• Orchestration Language: WDL (preferred), CWL, YAML, Nextflow, Snakemake

• Cloud: AWS, Azure, Google, AliBaba

• Programming Language: Java (preferred), Python, R

• Source control: GitLab (preferred), Bitbucket, GitHub, TFS

• Extensive analytic troubleshooting skills

• Excellent communication and organizational skills, especially for problem solving under pressure

• Strong technical documentation skills

• Eagerness to acquire new skills in genetics

• Ability to thrive in a fast-paced environment and manage multiple tasks independently

Preferred Technologies:

• High performance computing on a local cluster

• Bioinformatics Tools: GATK, SAMtools, bedtools, bwa, primer3, etc.

• Security / Privacy: HIPAA, GDPR

• Biology: Next-generation sequencing, Sanger sequencing, MLPA, PCR, Southern Blot

• Data science: Machine learning, deep neural networks