Bioinformatics Engineer

In the last year at Loka we helped clients advance the world’s #1 AI reading tutor, eliminate $1B in food waste and develop novel drugs for fighting cancer. To cap it off, at the end of 2024 Loka was recognized by AWS as Innovation Partner of the Year, outshining 150,000 partners for the title. And we did it all while enjoying every other Friday off 😎

As a Bioinformatics Engineer at Loka, you will design, build and maintain production-ready bioinformatics workflows and data infrastructures for Life Sciences customers, focusing on Genomics and other Omics domains.

You will work closely with data engineers, cloud architects and client teams to translate scientific requirements into scalable, repeatable and maintainable solutions. Preference will be given to MSc or PhD in Bioinformatics, Computational Biology, Biology, Bioengineering, Biomedical Engineering or a related field, or equivalent practical experience.

Join our team to feed your desire to grow, build with the latest tools and collaborate on projects that you can be proud of.

Responsibilities

• Design, implement and deploy bioinformatics workflows using languages such as Nextflow, WDL, Snakemake or similar.
• Define infrastructure and influence architectural decisions based on requirements and characteristics of pipelines being developed.
• Migrate pipelines and data processing workloads from on‑premises environments to AWS.
• Port and refactor existing pipelines between workflow orchestration languages and frameworks.
• Collaborate with the Data Engineering team to integrate bioinformatics pipelines into broader data platforms and products for Life Sciences and Omics use cases.
• Maintain and improve existing pipelines, including upgrades, performance optimizations and reliability enhancements.
• Provide expert bioinformatics support to clients, including troubleshooting, pipeline customization and best‑practices guidance.
• Stay current with emerging tools, standards and best practices in bioinformatics workflows, cloud-native architectures and Omics data analysis.

Required Skills

• MSc or PhD in Bioinformatics, Computational Biology, Biology, Bioengineering, Biomedical Engineering or a related field, or equivalent practical experience
• Experience developing reproducible bioinformatics workflows using Nextflow, Snakemake, WDL, CWL or similar workflow managers.
• Familiarity with AWS or other major cloud providers for running large‑scale bioinformatics workloads.
• Proficiency in Python and Shell.
• Experience using Docker and Conda (or mamba) for packaging and dependency management of bioinformatics tools and environments.

Nice to Have

• Hands-on experience building pipelines for genomics, transcriptomics or other NGS-based technologies (e.g. WGS, WES, bulk RNA‑seq, single‑cell RNA‑seq).
• Experience with commonly used tools for Omics data analysis (e.g. Cell Ranger, GATK, Salmon, VEP, OncoKB or similar).
• Familiarity with relevant bioinformatics data formats across primary, secondary and tertiary analysis (e.g. BCL, FASTQ, BAM/SAM, VCF, HDF5/h5ad).
• Experience with biological interpretation and tertiary analysis of Omics data (e.g. variant annotation and prioritization, pathway analysis, biomarker discovery).
• Exposure to large public genomic datasets and portals (e.g. GDC, TCGA, DepMap, gnomAD) and their typical usage patterns
  

Soft Skills

• Strong critical thinking skills, problem-solving ability and learning agility.
• Excellent written and oral communication skills.
• Ability to interact effectively with scientists and engineers in other disciplines with a positive and collaborative attitude.

Personality Profile

• Curious: You want to learn and grow in different industries utilizing a modern tech stack.
• Autonomous: You thrive in a fully remote, globally distributed team.
• Collaborative: You enjoy working as part of a team.
• Adaptable: You operate with a startup mindset and move at a startup pace.
• Dependable: You can be trusted to deliver high-quality work.

Benefits

• Every other Friday off (26 extra days off a year)
• Work wherever you’re most productive
• Explore and Relocation programs (three months work abroad or full international relocation)
• Paid sick days and local holidays
• Premium mental health subscriptions
• Access to LokaLabs™, our internal research and development program
• Fitness subscription
• Fitness and/or Mental Health Subscriptions
• Mental wellness programs
• Defined career path

Please submit your CV in English