Senior Software Engineer, Genomics

Feanix

. Build and operate Feanix’s genomics pipeline as a production system from sample through sequencing, alignment, imputation, genotyping, parentage, and trait results .

Posted 10/30/2026full-timeRemote • United StatesSenior💰 $180,000 - $220,000 per yearWebsite

Core Competencies

Role fit

Core Competencies

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Demonstrates expertise in building and operating genomics pipelines, with a strong focus on automation, sample tracking, and cost management. Proficient in genomic data handling and collaboration with scientific teams to ensure reliable and scalable systems.

Highest-signal resume keywords

Genomic Data FluencyPython ProgrammingBioinformatics Pipeline ManagementSample Tracking System DevelopmentCost Management for Large Data

ATS Keywords

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Applicant Tracking System Keywords

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Hard Skills

Genomic DataFASTQBAMVCFPLINKImputationIdempotent PipelinesCoding AgentsGenotype ImputationGenomic Prediction

Soft Skills

CollaborationCommunicationProblem-Solving

Tools & Technologies

TerraformOpenTofuLIMSS3

Industry Keywords

GenomicsBioinformaticsParentage VerificationSNP-based ParentageSequencing PipelinesAgriculture

Tech Stack

Tools & technologies

PythonTerraform

About the role

Key responsibilities & impact

Build and operate Feanix’s genomics pipeline as a production system from sample through sequencing, alignment, imputation, genotyping, parentage, and trait results
Automate pipeline scheduling and triggering, with retries, version pinning, monitoring, alerting, and observability
Lead development of an authoritative sample-state ledger tracking each sample’s processing status and failure reason
Move parentage fleet runs onto schedules with completion and lateness alerts
Bring genomics repositories onto the engineering CI and deployment path in partnership with infrastructure
Ensure pipeline and workflow versions are managed in code, tested, and reviewed
Establish cost-per-sample visibility for sequencing compute and storage
Define lifecycle policies for data measured in hundreds of terabytes
Manage lab and vendor intake from the in-house sequencer, outside sequencing labs, and genotyping-chip providers
Make breeding-value model training reproducible and repeatable
Lead production engineering for genomics and set engineering standards as the team grows
Scale genomics processing from 20+ farms to hundreds, improving volume, accuracy, reliability, and cost per sample
Collaborate with the founding genomics engineer, infrastructure engineer, scientists, and other engineers
Participate in the weekly on-call and triage rotation
Build alerting that keeps genomics on-call quiet
Report to the Platform Engineering Manager
Travel 15–20%, including visits to commercial dairies and Feanix headquarters in Scotts Valley, California

Requirements

What you’ll need

Several years running scientific or bioinformatics pipelines in production, scheduled, monitored, and depended on by people other than you
Fluency in genomic data, including FASTQ/BAM/VCF, PLINK, imputation (GLIMPSE, Beagle, or similar), and coverage and QC metrics
Experience building sample tracking, LIMS-like state, or another item-state system
Strong Python
Comfort with S3-scale data, idempotent pipelines, retries, and alerting
Cost awareness with large data, including storage lifecycle and compute spend per unit
Track record working alongside scientists and translating methods into reliable systems
Daily, load-bearing use of coding agents, and a real position on where they break down
Applicants must be authorized to work in the United States
Unable to offer visa sponsorship or transfers at this time
Preferred: livestock, plant, or human population genomics
Preferred: parentage or pedigree work, including SNP-based parentage verification, kinship, or reconciling pedigrees with genotypes
Preferred: production experience with genotype imputation or sequencing pipelines
Preferred: genomic prediction (GBLUP and relatives)
Preferred: LIMS or sample-tracking integration with a wet lab
Preferred: supporting a small team through rapid growth
Preferred: time at a sequencing lab or genomics service company
Preferred: Terraform/OpenTofu
Agriculture experience is not required

Benefits

Comp & perks

Medical coverage
Dental coverage
Vision coverage
401(k)
Pet insurance
Flexible paid time off
Paid parental leave, including 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 throughout the application and interview process