About Cambrian Bioworks
Cambrian Bioworks is an Indian life sciences company developing laboratory automation instruments and diagnostic products for clinical and research applications. We are building an integrated NGS infrastructure platform and are looking for a Bioinformatics Engineer to own our clinical pipeline development end-to-end.
Role Overview
This is a hands-on individual contributor role. You will design, build, validate, and maintain production-grade clinical NGS analysis pipelines from scratch. You own the code, the validation, and the output. This is a build role — not a maintain role.
What You Will Do
Pipeline Development
- Build and maintain clinical-grade NGS analysis pipelines covering multiple assay types — targeted panels, cfDNA, and exome
- Implement somatic and germline variant calling, CNV detection, fusion calling, and relevant biomarker calculations (TMB, MSI, aneuploidy)
- Integrate clinical annotation databases for variant classification and actionability tiering per established guidelines
- Containerise and version-control all pipelines for reproducibility and portability across compute environments
- Deploy pipelines on cloud or on-premise infrastructure using standard workflow managers
Validation & Quality
- Design and execute analytical validation studies — sensitivity, specificity, reproducibility — across all pipeline modules
- Build QC frameworks — coverage metrics, on-target rate, contamination detection, run-level and sample-level QC
- Maintain validation documentation suitable for regulatory and accreditation requirements
Integration & Reporting
- Integrate pipeline outputs with our internal workflow software for automated report generation and result delivery
- Build and maintain QC dashboards for pipeline monitoring across production runs
What We're Looking For
Must Have
- 4–7 years of hands-on experience building and deploying clinical NGS analysis pipelines — not configuring existing tools
- Production experience with somatic variant calling for targeted panels — GATK Mutect2 or equivalent, CNV callers, fusion detection
- Strong Python programming — pipeline logic, annotation scripts, QC automation
- Experience with workflow managers — Snakemake, Nextflow, or WDL
- Familiarity with clinical variant classification frameworks — AMP/ASCO/CAP, ACMG/AMP
- Docker/Singularity for pipeline containerisation
- Deep understanding of how NGS library prep variables affect downstream bioinformatics
Good to Have
- cfDNA pipeline experience — UMI processing, low allele frequency variant detection
- Chromosomal aneuploidy calling from cfDNA
- Cloud compute experience — AWS Batch, GCP Life Sciences, or equivalent
- Experience supporting NABL or CAP accreditation with bioinformatics validation data
- MSc or PhD in Bioinformatics, Computational Biology, or related field
Compensation
Competitive fixed compensation benchmarked to senior bioinformatics engineering talent in Bengaluru, commensurate with experience. ESOP included — this is a foundational role at a scaling company.
