Bioinformatics Engineer

Bioinformatics Engineer – Immune Repertoire & Transcriptomics Job Summary We are seeking experienced Bioinformatics Engineers with strong expertise in Immune Repertoire and Transcriptomics data processing to build and deploy scalable cloud-native bioinformatics workflows. The role involves developing production-grade pipelines for TCR/BCR sequencing, single-cell RNA-seq, and Bulk RNA-seq datasets, along with downstream analytics and multi-omics integration. Key Responsibilities Design, develop, and deploy scalable bioinformatics pipelines for: TCR/BCR sequencing data Single-cell RNA-seq (scRNA-seq) Bulk RNA-seq workflows Process sequencing datasets from platforms such as 10x Genomics, SMART-seq, Adaptive, and iRepertoire.

Build workflows for QC, alignment, pseudo-alignment, normalization, clustering, differential expression, clonotype analysis, diversity metrics, antigen/epitope matching, and pathway enrichment. Develop production-grade, containerized workflows using Docker/Singularity and workflow orchestration tools such as Nextflow, Snakemake, or WDL/Cromwell. Deploy and manage bioinformatics workflows in cloud environments, preferably GCP.

Implement CI/CD pipelines using GitHub Actions, GitLab CI, or similar tools. Integrate transcriptomics, immune repertoire, and metadata-driven datasets into downstream analytics and enterprise data platforms. Generate standardized analysis-ready outputs, QC dashboards, reports, and reproducible scientific workflows.

Collaborate with scientific, data engineering, and DevOps teams to translate biological requirements into scalable engineering solutions. Produce technical documentation, pipeline documentation, and conduct demos/workshops when required. Required Skills Strong hands-on experience with: TCR/BCR-seq scRNA-seq Bulk RNA-seq workflows Expertise in tools/frameworks such as: Cell Ranger, MiXCR, IgBlast, TRUST4, Immcantation Seurat, Scanpy, scRepertoire, Immunarch STAR, HISAT2, Salmon, Kallisto DESeq2, edgeR, limma Strong programming skills in Python and/or R.

Experience with Docker, CI/CD, cloud-native pipeline development, and workflow automation tools. Hands-on experience with GCP services and large-scale sequencing data processing. Familiarity with SQL and multi-omics data integration workflows.

Preferred Skills Experience with Terraform or Infrastructure as Code. Exposure to enterprise-scale genomics platforms and workflow orchestration systems. Strong communication and stakeholder management skills.

Experience 4+ Years Work Mode Remote