Principal Bioinformatics Engineer
Nextflow pipelines and Azure Batch infrastructure for genomics
I build production genomic pipelines for WGS, pathogen surveillance, and multi-omics, and fix the Azure Batch and HPC bottlenecks that stall them.
Book a Technical ReviewA bioinformatician who also runs the infrastructure
Bioinformatics engineer and consultant with a PhD and 15+ years in genomics. I write Nextflow and Snakemake pipelines and keep them running on Azure Batch and HPC clusters: the containerization, resource allocation, and cloud debugging that usually falls between the bioinformatics team and IT. Available for remote B2B work as an EU-based independent contractor (W-8BEN ready).
Core Services
Nextflow & Snakemake Pipeline Architecture
Reproducible pipelines for WGS, pathogen genomics, transcriptomics, AMR, and GMO tracking, built to run the same way on a laptop, an HPC cluster, or the cloud.
Azure Batch & HPC Troubleshooting
Deployment and debugging on Azure Batch and SLURM/SGE clusters. Docker containerization and resource tuning to cut cloud spend and clear the bottlenecks that stall large runs.
Scripting & Data Analytics
Automation and large-scale multi-omics data processing in Python, Bash, and R.
Case Study — European Food Safety Authority (EFSA)
WGS pipeline troubleshooting on Azure Batch
As an external contractor on EFSA's high-throughput WGS pipeline (bacteria, fungi, and viruses), I traced two problems the internal IT team had been unable to resolve: storage limits on the container batch images, and inefficient resource allocation during large genomic runs.
Debugging the Docker containerization and tuning nextflow.config parameters, including custom Docker image mounts to work around Azure VM storage limits and distribute the HPC workload more evenly.
Storage bottlenecks gone, wasted cloud compute cut, and a stable pipeline that now supports ongoing pathogen and AMR surveillance.
Technical Stack
Pipeline Engines
- Nextflow
- Snakemake
Infrastructure & DevOps
- Azure Batch
- HPC Clusters (SLURM/SGE)
- Docker
- Git
Languages
- Python
- Bash
- R
Domains
- Genomics
- Transcriptomics
- Metagenomics
- AMR
Let's scale your bioinformatics infrastructure.
If you have pipelines that need to move from a working prototype to something that runs reliably in production, get in touch.
Book a Technical Review ↗or send a message directly