Bioinformatics Associate II

Software Guidance & Assistance, Inc., (SGA), is searching for a Bioinformatics Associate II for a contract assignment with one of our premier Pharmaceutical clients in South San Francisco, CA.

Responsibilities :

• We are seeking a highly skilled and motivated Bioinformatician (Level II) with 5-10 years of hands-on experience and a Master's degree in Bioinformatics, Computational Biology, Genomics, Computer Science, or a related quantitative field.
• This individual will lead the development and optimization of bioinformatics pipelines, analyze NGS datasets, and collaborate closely with cross-functional research teams. The ideal candidate is highly proficient in Python or R, has deep experience with NGS workflows, and thrives in a fast-paced research environment.
• Bioinformatics Pipeline Development
  • 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.
• NGS Data Analysis
  • Perform advanced computational analyses including:
    • Variant calling
    • Differential gene expression
    • Transcriptomic and epigenomic analysis
    • Pathway/enrichment analysis
    • Genomic annotation
  • Conduct QC for FASTQ, BAM/CRAM, VCF, and related formats.
• Programming & Scripting
  • Write efficient, reproducible, and well-documented code in Python or R.
  • Build custom tools for data integration, transformation, and visualization.
• Tool & Algorithm Implementation
  • Implement, evaluate, and adapt existing bioinformatics tools and algorithms.
  • Integrate open-source resources to support project objectives.
• Cross-Functional Collaboration
  • 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.
• Troubleshooting & Optimization
  • Diagnose pipeline failures, data issues, and computational inefficiencies.
  • Ensure data integrity, workflow reproducibility, and methodological rigor.
• Documentation & Reporting
  • Prepare clear reports, visualizations, and presentations summarizing analysis outcomes.
  • Maintain precise documentation of workflows, code, and datasets.
• Continuous Learning
  • Stay current with bioinformatics tools, NGS technologies, and computational methods.

Required Skills:

• Master's degree is required (Bioinformatics, Computational Biology, Genomics, Computer Science, or related quantitative field).
• 5-10 years of hands-on experience working in bioinformatics or computational genomics.
• Demonstrated proficiency in Python or R (candidate must specify their primary language).
• Extensive experience analyzing NGS datasets and implementing standard workflows.
• Proficiency with key tools, including:
  • STAR, BWA, Bowtie2, GATK, Samtools, bcftools
  • DESeq2, EdgeR, Seurat, Scanpy
• Experience with public genomic databases (NCBI, Ensembl, UCSC, GTEx, TCGA).
• Strong understanding of statistics, experimental design, and computational biology principles.
• Proficiency using Git/GitHub for version control.
• Excellent communication, problem-solving, and organizational skills.

Preferred Skills:

• Experience with workflow management systems (Nextflow, Snakemake, WDL/Cromwell).
• Background in cloud computing (AWS, Google Cloud Platform, Azure) and containerization (Docker, Singularity).
• Previous work with HPC clusters.
• Experience with specialized sequencing applications such as:
  • Single-cell assays (scRNA-seq / ATAC-seq)
  • Long-read sequencing (PacBio, ONT)
  • Epigenomics assays

SGA is a technology and resource solutions provider driven to stand out. We are a women-owned business. Our mission: to solve big IT problems with a more personal, boutique approach. Each year, we match consultants like you to more than 1,000 engagements. When we say let's work better together, we mean it. You'll join a diverse team built on these core values: customer service, employee development, and quality and integrity in everything we do. Be yourself, love what you do and find your passion at work. Please find us at .

SGA is an Equal Opportunity Employer and does not discriminate on the basis of Race, Color, Sex, Sexual Orientation, Gender Identity, Religion, National Origin, Disability, Veteran Status, Age, Marital Status, Pregnancy, Genetic Information, or Other Legally Protected Status. We are committed to providing access, equal opportunity, and reasonable accommodation for individuals with disabilities in employment, and our services, programs, and activities. Please visit our company to request an accommodation or assistance regarding our policy
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