Bioinformatics Associate II

Bioinformatics Associate II – South San Francisco, CA | W2 Contract (6 months)

BEPC Inc. is actively looking for a Bioinformatics Associate II to join our client’s site in South San Francisco, CA. This 6‑month W2 contract role will support the development and optimization of bioinformatics pipelines, NGS data analysis, and close collaboration with cross‑functional research teams.

Pay Rate: $60.85 – $64.85 /hour (determined based on experience, paid weekly)

Work Model: Hybrid – South San Francisco (1 day onsite / 4 days remote)

Benefits include: medical, dental, vision, and life insurance.

Required knowledge: Programming language (Python or R). This is a W2‑only role – C2C or C2H will not be considered.

• Develop, automate, and maintain robust pipelines for RNA‑seq, WGS/WES, scRNA‑seq, or other sequencing datasets.
• Optimize workflows for reproducibility, scalability, and performance across HPC or cloud environments.
• Perform advanced computational analyses including variant calling, transcriptomic and epigenomic analysis, and genomic annotation.
• Conduct quality control for FASTQ, BAM/CRAM, VCF, and related formats.
• Write efficient, reproducible, and well‑documented code in Python or R, and build custom tools for data integration, transformation, and visualization.
• Implement, evaluate, and adapt existing bioinformatics tools and algorithms and integrate open‑source resources to support project objectives.
• Work closely with wet‑lab scientists to interpret data, troubleshoot issues, and align computational analyses with experimental design.
• Communicate complex findings clearly to technical and non‑technical audiences.
• Diagnose pipeline failures, data issues, and computational inefficiencies, ensuring data integrity, workflow reproducibility, and methodological rigor.
• Prepare clear reports, visualizations, and presentations summarizing analysis outcomes; maintain precise documentation of workflows, code, and datasets.
• Stay current with bioinformatics tools, NGS technologies, and computational methodology.

• Master’s degree required (Bioinformatics, Computational Biology, Genomics, Computer Science, or related quantitative field).
• 5–10 years of hands‑on experience in bioinformatics or computational genomics.
• Demonstrated proficiency in Python or R (candidate must specify primary language).
• Extensive experience analyzing NGS datasets and implementing standard workflows.
• Strong understanding of statistics, experimental design, and computational biology principles.
• Proficiency using Git/Git Hub for version control.
• Excellent communication, problem‑solving, and organizational skills.

• Experience with workflow management systems (Nextflow, Snakemake, WDL/Cromwell).
• Background in cloud computing (AWS, GCP, Azure) and containerization (Docker, Singularity). /li>
• Previous work with HPC clusters.
• Experience with specialized sequencing applications.

BEPC Inc., founded in 2007, is a 100% employee‑owned company providing consulting and staffing solutions across technologies, engineering, manufacturing, and project management. We foster a collaborative environment where our team members thrive. Competitive benefits include medical, dental, vision, and life insurance.

Apply Now! Qualified candidates are encouraged to submit an up‑to‑date resume that highlights how your experience aligns with the role. Please include specific examples that demonstrate your qualifications. We look forward to connecting with you!