Director, Automation & Data Engineering

Congenica; France; Hybride; EUR 60 000 - 81 000; Plein temps

Résumé du poste

SeqOne is seeking a Director, Automation & Data Engineering to own the platform, drive automation and data tooling across the SeqOne Platform, including Nexus BI, Clinical Data Curation ETL, SeqOne Flow Premium, API Gateway, and internal tooling.

You will lead a 5-person team, partner with CTO and Deputy CTO, oversee enterprise HL7/FHIR/LIMS integrations, ensure ISO 13485/27001 compliance, and shape scalable, compliant architectures. Hybrid Paris or Montpellier.

Qualifications

• 6-8 years of software engineering experience with data engineering, backend development, ETL, or platform engineering.
• 3+ years of proven team leadership experience managing engineers.
• Proficiency in Python, SQL, and API design; experience with Airflow and N8N.
• Cloud infrastructure experience (AWS); comfortable with Docker and Kubernetes.
• Experience with HL7/FHIR interfaces and LIMS integrations is highly valued.
• Knowledge of ISO 13485/27001 and GDPR compliance is a plus.

Responsabilités

• Platform Product Ownership: build internal products for operational excellence and customer success.
• Strategic Customer Engineering: advise on integrations, design architectures, support deployments.
• Team Leadership & Operations: manage a 5-person team, plan capacity, ensure quality and delivery.
• Main tasks: own BI/analytics, ETL pipelines, SeqOne Flow Premium, API tooling, and platform integration gaps.

Connaissances

Data pipelines

ETL architecture

Python

SQL

API design

Airflow

N8N

HL7/FHIR

LIMS integration

Leadership

Team management

Communication

Outils

Airflow

N8N

Docker

Kubernetes

AWS

Description du poste

Full-time, Permanent Paris or Montpellier (Hub-based, Hybrid)

Director, Automation & Data Engineering

About SeqOne

SeqOne is a fast-growing B2B software scale-up building the leading cloud platform for clinical next-generation sequencing (NGS) analysis.

What is clinical NGS, and why does it matter?

Next-generation sequencing has revolutionised medicine by making it possible to read a patient's genetic code quickly and affordably. But raw sequencing data is meaningless on its own—it must be processed, filtered, annotated, and interpreted before a clinician can act on it. This interpretation step is now the bottleneck in precision medicine: labs are drowning in data while patients wait for answers.

SeqOne exists to solve this. Our cloud-based software platform helps molecular laboratories and hospitals analyse, interpret, and report genetic data—faster, more accurately, and at scale. We combine advanced bioinformatics pipelines, AI-powered decision support, and intuitive clinical workflows into a single SaaS solution, enabling labs to focus on what matters: delivering actionable insights to patients and their care teams.

With 170+ customers across 32 countries, SeqOne supports cancer diagnostics, rare disease diagnosis, pharmacogenomics, and newborn screening—anywhere precision medicine is needed.

But here's what we're really doing:

We're compressing the time between a patient's uncertainty and their answer.

A child waiting for a rare disease diagnosis. A cancer patient waiting to learn if a targeted therapy might work. A family waiting to understand. The sequencers are not the bottleneck anymore—interpretation is. That's the problem SeqOne exists to solve.

Our north star is a 10x reduction in human time from "case ready for review" to "report signed." Every click is a cost. Every manual step is a bug we haven't fixed yet. Every repeated pattern is a failure of automation.

If we build SeqOne right, labs will one day struggle to remember how they ever did this work without it.

The organization context:

• Total Technology & Engineering headcount: ~45 people across Platform, Stream-aligned, Subsystem, and Enabler teams
• CTO Organization: ~30 people including Engineering FullStack (~12), Engineering QA (~7), Platform Infrastructure (~4), Biocore (~4), BioOps (~3)
• Your Platform team: 5 people (3 existing: Senior Bioinformatician for data curation + Automation Engineer for N8N/SeqOne Flow, 1 public API architect), 1 to hire: Data Engineer, 1 prospective nearshore resource

Our Values

• Unstoppable Positivity – We approach challenges with energy, resourcefulness and a solution-first mindset, turning constraints into opportunities instead of getting stuck in complaints. We value people who learn from setbacks, iterate quickly and keep moving forward even when things are ambiguous or hard.
• Customer Pulse – Our customers operate in healthcare, and their work has a direct impact on patients' lives, so understanding their reality and anticipating their needs is central to our mission. We build long-term, trust-based relationships, react quickly to issues and keep quality and regulatory expectations at the heart of what we do.
• Excellence Explorers – We are driven by curiosity, high standards and measurable impact, treating excellence as an ongoing journey rather than a fixed target. We prioritise what really moves the needle, rely on data to guide decisions, and challenge the status quo to reach world-class levels in our products, services and operations.
• Open Heart, Hands-On – We combine kindness, humility and direct feedback with a strong sense of ownership and reliability. We help each other succeed, speak up honestly even when conversations are uncomfortable, and follow through on our commitments because everyone's work is interconnected.

Responsibilities

1) Platform Product Ownership (50%)

Build the internal products that enable SeqOne's operational excellence and customer success.

• Nexus BI & Internal Analytics: Architect and evolve data pipelines feeding internal analytics dashboards (platform usage metrics, customer TAT analysis, unit economics). Enable data-driven decisions for Product, Commercial, and Operations teams.
• Clinical Data Curation Platform: Own the ETL infrastructure (Airflow-based/can evolve) that aggregates and curates clinical knowledge databases (ClinVar, gnomAD, population databases, gene panels; …). Ensure data freshness, accuracy, and regulatory auditability (ISO 13485 compliance, and up to date licenses/contracts).
• SeqOne Flow Premium: Lead development of the customer-facing automation engine that integrates SeqOne Platform into lab environments (file upload/download, analysis triggering, LIMS connectors, HL7/FHIR interfaces). Transform one-off integrations into reusable, self-service modules using N8N workflow orchestration.
• API Gateway & Developer Experience: Treat APIs as products. Ensure comprehensive documentation, SDKs, sandbox environments, and self-service tooling that enable customer IT teams to integrate autonomously with Public API. Reduce dependency on professional services.
• Platform Operations Tooling: Own internal admin tools supporting customer management, and operational workflows.

2) Strategic Customer Engineering (30%)

Be the technical expert customers meet when SeqOne Automation implementations require deep integration.

• Pre-Sales Technical Advisory: Partner with Commercial teams to demonstrate SeqOne's automation capabilities during enterprise sales cycles. Present integration architectures to CTOs, IT Directors, and Lab Managers.
• Complex Integration Design: Design solution architectures for strategic accounts requiring custom LIMS integrations, HL7/FHIR interfaces, or complex workflow automation. Balance customer constraints (TAT requirements, privacy regulations, legacy systems) with platform scalability.
• Implementation Support: Oversee technical onboarding for SeqOne Flow Premium customers from contract signature to production go-live. Coordinate with Customer Success to meet SLA commitments.
• Product Feedback Loop: Channel customer implementation learnings back into platform capabilities that benefit all customers. Turn bespoke solutions into self-service features.

3) Team Leadership & Operations (20%)

Build and scale a product-minded Automation & Data team.

• Team Management: Lead and develop 5 direct reports including Senior Bioinformatician (clinical data curation), Senior Data Engineer (to hire - BI/ETL infrastructure), Automation Engineers (N8N/Flow development), and prospective nearshore resources.
• Capacity Planning & Delivery: Orchestrate multiple parallel workstreams (internal platform roadmap + customer implementation support). Balance build vs. support work. Ensure predictable delivery cadence aligned with Team Topologies principles.
• Operational Excellence: Define engineering standards, "Definition of Done," incident response protocols. Ensure compliance with ISO 13485 and ISO 27001 requirements for platform tooling where needed.
• Talent Development: Hire missing skills (Data Engineer, Bioinformatician), mentor team members, define career paths and technical excellence standards.

Main tasks carried out

• Architect, build, and maintain internal BI/analytics infrastructure (Nexus) providing visibility into platform performance, customer usage patterns, and operational metrics
• Own and evolve clinical data curation ETL pipelines (Airflow) ensuring production-ready reference databases (ClinVar, gnomAD, gene panels, population frequencies)
• Lead SeqOne Flow Premium development: N8N-based workflow automation, LIMS connectors, file transfer automation, analysis triggering APIs
• Design and implement API-as-a-Product capabilities: comprehensive documentation, SDKs, developer sandbox environments, self-service integration tooling
• Collaborate with Deputy CTO on CRD platform integration gaps and migration planning (limited scope - strategic alignment only)
• Partner with Platform Infrastructure Director on data storage, compute resources, and observability infrastructure
• Work closely with VP Engineering to ensure platform capabilities serve FullStack team needs and reduce their cognitive load
• Engage with CPO and Product Owners to understand internal product requirements from stream-aligned teams (Rare & Hereditary, Oncology, Preventive & Growth, Clinical Workflow)
• Represent SeqOne in pre-sales technical discussions for complex enterprise accounts requiring custom automation/integration
• Manage team operations: sprint planning, code reviews, technical documentation, on-call rotations, incident post-mortems
• Recruit, onboard, and develop engineering talent (Data Engineers, Bioinformaticians, Automation Engineers)
• Ensure all platform tooling meets medical device software quality standards (IEC 62304) and information security requirements (ISO 27001)

Qualifications

• 6-8 years of software engineering experience with focus on Data Engineering, Backend Development, ETL/Data Pipelines, or Platform Engineering
• Proven team leadership experience: 3+ years managing engineers (hiring, mentoring, performance management)
• Technical depth: Strong proficiency in Python, SQL, and API design. Experience with workflow orchestration tools (Airflow, N8N or similar)
• Cloud infrastructure experience: AWS preferred. Comfortable with Docker, Kubernetes
• Data engineering fundamentals: ETL pipeline design, data warehousing concepts, data quality/validation frameworks
• Integration experience: REST APIs, HL7/FHIR standards (healthcare interoperability), LIMS integration background highly valued
• B2B SaaS or HealthTech experience preferred: Understanding of enterprise customer needs, especially in regulated industries
• Customer-facing capability: Comfortable presenting technical solutions to CTOs, IT Directors, Lab Managers. Can translate complex technical concepts for non-technical stakeholders
• Regulatory awareness: Familiarity with ISO 13485, ISO 27001, GDPR, or similar compliance frameworks is a strong plus
• Bioinformatics literacy (nice-to-have): Basic understanding of NGS data (VCFs, FASTQs), reference genome versions (hg19/hg38), clinical genomics workflows. Not required - can be learned on the job with team support.

Skills

• Technical Skills:
  • Deep expertise in data pipelines, ETL architecture, and workflow orchestration (Airflow or equivalent)
  • Proficiency in Python (data processing, automation, API development) and SQL (PostgreSQL preferred)
  • Experience building internal developer platforms or tooling that other engineers consume
  • Strong API design skills: RESTful principles, documentation-first approach, SDK development
  • Understanding of BI/analytics infrastructure: data modeling, metrics definition, dashboard design
  • Integration patterns: Experience with N8N (or similar workflow tools), LIMS connectors, HL7/FHIR interfaces, file-based integrations
  • Cloud-native development: AWS services (S3, Lambda, RDS, ECS), infrastructure-as-code mindset
  • Knowledge of data quality frameworks: validation, lineage tracking, error handling, monitoring
• Leadership & Soft Skills:
  • Product-minded engineering: Treats internal tools as products with users, roadmaps, and success metrics. Prioritizes reusability and self-service over one-off solutions
  • Team leadership: Experience building and scaling engineering teams through growth phases. Able to balance hands-on technical work with people management
  • Platform team mindset: Understands Team Topologies principles. Naturally reduces cognitive load for stream-aligned teams. Thinks in terms of "internal customers" and developer experience
  • Stakeholder management: Bridges technical teams with business stakeholders. Equally comfortable in architecture discussions and commercial conversations
  • Customer empathy: Can step into pre-sales technical advisory or post-sales implementation support when complex integrations require deep expertise
  • Strategic thinking: Balances short-term customer needs with long-term platform scalability. Knows when to build bespoke vs. when to standardize
  • Communication excellence: Fluent English required (written and spoken - documentation, customer interactions, international team collaboration). French helpful but not required
  • Scale-up adaptability: Thrives in fast-paced environments. Comfortable with ambiguity, changing priorities, and building structure where none exists
  • Passion for impact: Motivated by enabling others' success. Finds satisfaction in building tools that make colleagues' and customers' lives easier

Job Types

Full-time, Permanent

Pay

From 70,000.00€ per year

Work Location

Hybrid or remote in Paris or Montpellier