Job Overview We are seeking a bioinformatician to support and maintain production next-generation sequencing (NGS) pipelines within a clinical pathology lab. This role focuses on reliable, compliant processing of genomic data, variant analysis, and integration with reporting systems.

In addition to core production responsibilities, there will be opportunities to contribute to internal research efforts, including exploratory analyses and dissemination of findings. Responsibilities Run, monitor, and maintain NGS analysis pipelines (alignment, variant calling, QC) Troubleshoot pipeline failures and ensure reproducibility and consistency of results Implement and manage workflows (e.g., Nextflow or Snakemake) Process sequencing data in a cloud environment (

AWS:

S3, EC2, Batch) Validate and document pipelines in accordance with

CLIA/CAP

requirements Ensure HIPAA-compliant handling of genomic and patient data Integrate analysis outputs with LIS/LIMS and reporting systems Perform variant annotation and support interpretation workflows Interpret results and discuss with Pathologist Maintain audit trails, versioning, and data provenance for all analyses Collaborate with laboratory staff to meet turnaround time requirements Perform statistical analysis and data exploration using Python and R Contribute to internal research initiatives, including method evaluation and exploratory studies Assist in preparation of abstracts, posters, and manuscripts based on lab-generated data Required Qualifications Bachelor's or Master's degree in Bioinformatics, Computational Biology, or related field Strong programming skills in Python (primary language) Working knowledge of R for statistical analysis and visualization Experience with NGS data processing (FASTQ →

BAM/CRAM

→ VCF) Familiarity with standard bioinformatics tools (e.g., BWA, GATK, samtools, bcftools) Experience with workflow management systems (Nextflow or Snakemake) Experience working in Linux environments and shell scripting Familiarity with AWS (e.g., S3, EC2, Batch), Azure, or similar cloud platforms Strong problem-solving skills and attention to detail Ability to communicate technical concepts effectively across multidisciplinary teams Preferred Qualifications Experience working in a CLIA/CAP-regulated laboratory environment Familiarity with variant annotation tools (e.g., VEP, ANNOVAR) Experience integrating bioinformatics workflows with

LIS/LIMS

systems Understanding of clinical reporting workflows for genomic data Experience contributing to scientific publications, posters, or presentations Familiarity with experimental design and analysis in genomics research Ability to translate research methods into production-ready workflows Work Environment Small, collaborative clinical laboratory setting Combination of production support and research-oriented work Opportunity to directly impact patient care through reliable genomic analysis Exposure to cloud-based infrastructure and modern bioinformatics tooling Summary This role is best suited for a bioinformatician who is comfortable operating production pipelines in a regulated environment, while also contributing to targeted research efforts. The primary focus is on delivering accurate, reproducible, and compliant genomic analyses that support clinical decision-making.

Pay:

$22.00 - $28.00 per hour

Benefits:

401(k) Dental insurance Free parking Health insurance Life insurance Paid time off Vision insurance

Work Location:

In person