Bioinformatician, Viral Genomics & Diagnostics

Primary.Health; San Francisco (CA); Remote; USD 117,000 - 138,000; Part time

Job summary

Primary.Health is seeking an experienced bioinformatician for an on-demand, part-time retainer to analyze viral sequence data and track variants. This remote role requires independence and the ability to translate complex genomic findings for stakeholders.

You will run pipelines for alignment and lineage assignment, assess diagnostic implications of sequence changes, and monitor global surveillance data. Flexible scheduling applies, with potential bursts during outbreaks.

Qualifications

• Advanced degree in Bioinformatics, Computational Biology, or related field (or equivalent experience).
• 3+ years of hands-on viral or pathogen genomics experience.
• Proficiency in Python and/or R and standard genomics tools (e.g., Nextclade, Pangolin, Nextstrain).

Responsibilities

• Analyze viral genomes to identify mutations, lineages, and variants of concern.
• Assess the impact of sequence changes on assay performance (primer/probe binding, sensitivity).
• Run and maintain reproducible pipelines for alignment, variant calling, and lineage assignment.
• Summarize findings clearly for non-technical stakeholders.
• Monitor CDC, WHO, and GISAID surveillance and flag relevant developments.

Skills

Genomics analysis

Bioinformatics

Data interpretation

Education

Advanced degree in Bioinformatics or related field

Tools

Python

R

Nextclade

Pangolin

Nextstrain

Job description

About Primary

Primary.Health is committed to protecting the health of every community through easy and affordable access to diagnostics. We provide program management software and program design services that let employers, schools and communities administer testing to prevent the spread of communicable diseases.

JOB SCOPE

We are seeking an experienced bioinformatician on a part-time retainer to analyze viral sequence data, track emerging variants, and advise on how genomic changes may affect our diagnostic tests. Scheduling is flexible, with faster turnaround occasionally needed during outbreaks or new variant emergence.

MAJOR JOB DUTIES

• Analyze viral genomes (e.g., SARS-CoV-2, influenza, RSV) to identify mutations, lineages, and variants of concern.
• Assess the impact of sequence changes on assay performance (primer/probe binding, sensitivity).
• Run and maintain reproducible pipelines for alignment, variant calling, and lineage assignment.
• Summarize findings clearly for non-technical stakeholders.
• Monitor CDC, WHO, and GISAID surveillance and flag relevant developments.

QUALIFICATIONS

• Advanced degree in Bioinformatics, Computational Biology, or related field (or equivalent experience).
• 3+ years of hands-on viral or pathogen genomics experience.
• Proficiency in Python and/or R and standard genomics tools (e.g., Nextclade, Pangolin, Nextstrain).
• Experience evaluating molecular diagnostics against sequence variation preferred.
• Strong written communication; comfortable working independently on a part-time schedule.

Compensation

This role will be paid at $85.00–$100.00/hour on a 10-hour weekly retainer, with additional hours billed at the agreed hourly rate. Primary.Health provides an estimate of compensation as required by state regulations. Compensation may vary based on location, skills, qualifications, and experience, and is subject to change as new market data becomes available. Primary.Health reserves the right to modify this information at any time, subject to applicable law.

JOB TITLE: On-Demand Bioinformatician – Viral Genomics
JOB TYPE: Contract (1099) | 10 hours/week retainer
LOCATION: Remote
REPORTING TO: Head of Strategic Initiatives

Primary embraces diversity. We are proud to be an equal opportunity workplace and do not discriminate on the basis of sex, race, color, age, sexual orientation, gender identity, religion, national origin, citizenship, marital status, veteran status, or disability status. Pursuant to the San Francisco Fair Chance Ordinance, we will consider for employment qualified applicants with arrest and conviction records.