Job Description

Job Title: Bioinformatics Analyst

Location: South San Francisco, CA 94080

• Hybrid (South San Francisco, CA) or Remote (Pacific Time Zone or US-friendly time zone)

Employment Type: W2 Contract, 6 Month Contract with possibility for extensions

Pay Rate: $50.00 – $54.95 per hour

Work Schedule: Monday – Friday

Role Overview:

BEPC is seeking a Bioinformatics Analyst to support our client’s genomics initiatives focused on increasing diversity in genetic datasets. This role involves developing and maintaining analytical pipelines for long-read sequencing data, including methylation and whole-genome sequencing (WGS).

The ideal candidate will have hands-on experience with NGS pipelines, strong programming skills, and the ability to collaborate across global teams in a dynamic research environment.

Key Responsibilities:

• Develop and maintain bioinformatics pipelines for long-read sequencing (Oxford Nanopore) and methylation data.
• Execute workflows for data ingestion, processing, and interpretation .
• Perform quality control (QC) at multiple stages and identify data anomalies.
• Conduct variant calling and methylation analysis .
• Maintain clear documentation of pipelines, QC metrics, and code using Git.
• Collaborate with global teams to ensure smooth data transfer and reporting .
• Serve as a technical point of contact for data operations and workflow execution .

Qualifications:

• Bachelor’s or Master’s degree in Bioinformatics, Computational Biology, or related field.
• 2+ years of hands-on bioinformatics experience .
• Proficiency in Python and shell scripting (Bash) .
• Experience with HPC or cloud platforms (AWS) .
• Strong experience with NGS pipelines (Nextflow, Snakemake, or similar).
• Hands-on experience with human WGS data , especially Oxford Nanopore (ONT) .
• Experience with variant calling, basecalling, or methylation analysis .
• Familiarity with Git for version control and documentation .

Preferred Qualifications:

• Knowledge of T2T reference standards or pangenome graphs .
• Experience working in collaborative, global research environments .
• Strong communication skills and ability to work across multiple time zones .

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