R&D SOW 530641

You join the R&D Data Science team of a large pharmaceutical company.

The team already relies on many in-house bioinformatics pipelines: genome assembly, taxonomic classification, phase variation analysis, variant detection, epitope mimicry and more. Your role: migrate these tools to a cloud HPC environment, automate them and make them production-ready.

You will also build a new PCR primer and probe design tool from scratch, validated through in silico PCR, and hand it over to the team with its documentation and maintenance plan.

Migration to cloud HPC

• Migrate four existing pipelines (epitope mimicry, genome assembly, phase variation, taxonomic classification) to cloud HPC, ensuring identical results.
• Containerise the tools (Docker, Singularity/Apptainer) and adapt them to the cluster scheduler.

NGS analysis automation

• Automate sequencing data preprocessing and quality control (FastQ) and scale up read-mapping pipelines.
• Implement or adapt contaminant detection, consensus-building and variant-prediction pipelines.
• Automate antigen-diversity analysis, variant monitoring and paralogous-gene extraction.
• Improve the internal BIGSdb database and refactor existing post-analysis code.

New PCR assay design tool

• Define requirements, architecture and reference database strategy with end users.
• Develop primer and probe design pipelines, and in silico PCR pipelines (inclusivity, specificity).
• Validate the delivered tools (reproducibility, acceptance criteria) and prepare their deployment package.
• Write the documentation (reports, user guides, tutorials) and the maintenance plan.

Must-have

• Master's degree or PhD in bioinformatics, computational biology or a related field.
• At least 5 years of experience in bioinformatics engineering.
• Fluent Python (R is a plus), Linux and Git.
• Strong command of Nextflow or Snakemake.
• Containers (Docker, Singularity/Apptainer), HPC (Slurm) and cloud (AWS or Azure).
• Hands-on NGS analysis experience: quality control, read mapping, assembly, variant calling.
• Fluent professional English.

Nice-to-have

• Bacterial or pathogen genomics.
• PCR primer and probe design, in silico PCR, BIGSdb / PubMLST.
• Experience in a regulated pharma environment (GxP)