Senior Software Engineer, Genomics

This is a fully remote position, open to applicants in United States.

📋 Description

• Develop and manage Feanix’s genomics pipeline as a production system from sample collection through sequencing, alignment, imputation, genotyping, parentage, and trait analysis.

• Automate the scheduling and triggering of the pipeline, incorporating retries, version control, monitoring, alerting, and observability features.

• Spearhead the creation of an authoritative sample-state ledger to track the processing status and failure reasons for each sample.

• Transition parentage fleet runs onto schedules, incorporating completion and lateness alerts.

• Integrate genomics repositories into the engineering CI and deployment processes in collaboration with the infrastructure team.

• Ensure that pipeline and workflow versions are managed through code, rigorously tested, and subject to review.

• Establish visibility into cost-per-sample for sequencing compute and storage.

• Define lifecycle policies for data measured in hundreds of terabytes.

• Oversee lab and vendor intake from both the in-house sequencer and external sequencing labs and genotyping-chip providers.

• Create reproducible and repeatable breeding-value model training processes.

• Lead production engineering efforts in genomics and establish engineering standards as the team expands.

• Scale genomics processing from over 20 farms to hundreds, enhancing volume, accuracy, reliability, and cost efficiency per sample.

• Collaborate with the founding genomics engineer, infrastructure engineer, scientists, and other engineers.

• Participate in the weekly on-call and triage rotation.

• Develop alerting systems that maintain a quiet on-call environment for genomics.

• Report directly to the Platform Engineering Manager.

• Willingness to travel 15–20%, including visits to commercial dairies and Feanix headquarters in Scotts Valley, California.

⛳️ Requirements

• Several years of experience running scientific or bioinformatics pipelines in a production environment, which are scheduled, monitored, and relied upon by individuals other than yourself.

• Proficient understanding of genomic data formats, including FASTQ/BAM/VCF, PLINK, imputation (GLIMPSE, Beagle, or similar), as well as coverage and QC metrics.

• Experience in creating sample tracking systems, LIMS-like state management, or similar item-state systems.

• Strong proficiency in Python programming.

• Comfortable working with S3-scale data, idempotent pipelines, retries, and alerting mechanisms.

• Awareness of costs associated with large datasets, including storage lifecycle and compute expenses per unit.

• Proven track record of collaborating with scientists and translating methods into dependable systems.

• Regular, load-bearing use of coding agents, with a clear understanding of potential breakdown points.

• Applicants must possess authorization to work in the United States.

• Currently unable to provide visa sponsorship or transfers.

• Preferred qualifications include experience in livestock, plant, or human population genomics.

• Preferred experience with parentage or pedigree work, including SNP-based parentage verification, kinship analysis, or reconciling pedigrees with genotypes.

• Preferred background in production with genotype imputation or sequencing pipelines.

• Preferred knowledge of genomic prediction methods (GBLUP and related techniques).

• Preferred experience with LIMS or sample-tracking integration in a wet lab setting.

• Preferred experience supporting a small team through rapid growth.

• Preferred background working in a sequencing lab or genomics service company.

• Preferred familiarity with Terraform/OpenTofu.

• Agriculture experience is not a requirement.

🏝️ Benefits

• Medical coverage.

• Dental coverage.

• Vision coverage.

• 401(k) plan.

• Pet insurance.

• Flexible paid time off.

• Paid parental leave, offering up to twelve weeks of paid leave and/or supplemental pay coordination with applicable state benefits.

• Equity options.

• Flexible, remote-friendly work environment.

• Equal opportunity employer.

• Reasonable accommodations provided throughout the application and interview process.