Senior Software Engineer, Genomics

Feanix Biotechnologies builds genomic tools for animal breeding and herd management. The Senior Software Engineer, Genomics will lead the production engineering of genomics pipelines, automating and scaling their operation while improving reliability, speed, and cost per sample.

Responsibilities:

• The genomics pipeline as a production system. Sample → sequence → align → impute → genotype → parentage/trait, scheduled or triggered by new data, with retries, version pinning, and alerting
• A sample-state ledger. One authoritative record per sample of where it is (received, sequenced, passed coverage, imputed, called) and, if it stopped, why
• Parentage, end to end. Our parentage results already reach farms, built on the same genotypes, sample identities, and compute as the rest of genomics, so the team owns it end to end, from sample to result. You’d move fleet runs onto a schedule with completion and lateness alerts, and finish the readiness work that makes our already-built successor runner the system of record
• CI and deploys, in partnership with infrastructure. Our infrastructure engineer designs the CI and deploy path across engineering. You’d work with them to bring the genomics repositories onto it, so every change is tested and every pipeline and workflow version is managed in code and reviewed
• Cost and storage. A cost-per-sample view for sequencing compute and storage, and a lifecycle policy for data measured in hundreds of terabytes
• Lab and vendor intake. The handoff from our in-house sequencer, outside sequencing labs, and genotyping-chip providers into the pipeline
• Reproducible model training. Making breeding-value model training runnable and repeatable, so time goes to methods, not reruns

Requirements:

• Applicants must be authorized to work in the United States. We are unable to offer visa sponsorship or transfers at this time
• Several years running scientific or bioinformatics pipelines in production (Nextflow, AWS HealthOmics or Batch, or similar), scheduled, monitored, and depended on by people other than you
• Enough fluency in genomic data to debug it: FASTQ/BAM/VCF, PLINK, imputation (GLIMPSE, Beagle, or similar), and coverage and QC metrics
• Experience building sample tracking, LIMS-like state, or another “where is every item, and why” system
• Strong Python, and comfort with S3-scale data, idempotent pipelines, retries, and alerting
• Cost awareness with large data: storage lifecycle and compute spend per unit
• A track record of working alongside scientists, translating methods into reliable systems and asking good questions about them
• Daily, load-bearing use of coding agents, and a real position on where they break down
• Livestock, plant, or human population genomics
• Parentage or pedigree work: SNP-based parentage verification, kinship, or reconciling recorded pedigrees with genotypes
• Production experience with genotype imputation or sequencing pipelines (alignment, variant calling)
• Genomic prediction (GBLUP and relatives); useful, not expected
• LIMS or sample-tracking integration with a wet lab
• Having supported a small team through a period of rapid growth
• Time at a sequencing lab or genomics service company
• Terraform/OpenTofu
• Agriculture experience isn't required, but an interest doesn't hurt