Bioinformatics Engineer

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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

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