R&D SOW 530641

pYou join the RD 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. /p h3Responsibilities /h3 h3Migration to cloud HPC /h3 ul liMigrate four existing pipelines (epitope mimicry, genome assembly, phase variation, taxonomic classification) to cloud HPC, ensuring identical results. /li liContainerise the tools (Docker, Singularity/Apptainer) and adapt them to the cluster scheduler. /li /ul h3NGS analysis automation /h3 ul liAutomate sequencing data preprocessing and quality control (FastQ) and scale up read-mapping pipelines. /li liImplement or adapt contaminant detection, consensus-building and variant-prediction pipelines. /li liAutomate antigen-diversity analysis, variant monitoring and paralogous-gene extraction. /li liImprove the internal BIGSdb database and refactor existing post-analysis code. /li /ul h3New PCR assay design tool /h3 ul liDefine requirements, architecture and reference database strategy with end users. /li liDevelop primer and probe design pipelines, and in silico PCR pipelines (inclusivity, specificity). /li liValidate the delivered tools (reproducibility, acceptance criteria) and prepare their deployment package. /li liWrite the documentation (reports, user guides, tutorials) and the maintenance plan. /li /ul h3Requirements /h3 h3Must-have /h3 ul liMaster's degree or PhD in bioinformatics, computational biology or a related field. /li liAt least 5 years of experience in bioinformatics engineering. /li liFluent Python (R is a plus), Linux and Git. /li liStrong command of Nextflow or Snakemake. /li liContainers (Docker, Singularity/Apptainer), HPC (Slurm) and cloud (AWS or Azure). /li liHands-on NGS analysis

experience:
quality control, read mapping, assembly, variant calling. /li liFluent professional English. /li /ul h3Nice-to-have /h3 ul liBacterial or pathogen genomics. /li liPCR primer and probe design, in silico PCR, BIGSdb / PubMLST. /li liExperience in a regulated pharma environment (GxP) /li /ul