Position Title: Bioinformatician (Level II)
Work Location: South San Francisco, CA, 94080
Assignment Duration: 6 Months
Work Arrangement: Hybrid (1 day onsite / 4 days remote)

Position Summary:
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.

Key Responsibilities:
• 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
• Differential gene expression
• Transcriptomic and epigenomic analysis
• Pathway/enrichment analysis
• Genomic annotation

• Conduct QC for FASTQ, BAM/CRAM, VCF, and related formats.
• Write efficient, reproducible, and well-documented code in Python or R.
• Build custom tools for data integration, transformation, and visualization.
• Implement, evaluate, and adapt existing bioinformatics tools and algorithms.
• 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.
• Ensure 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 methods.

Qualification & Experience:
• 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.

Additional Information:
Experience with workflow management systems (Nextflow, Snakemake, WDL/Cromwell). Background in cloud computing (AWS, GCP, 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

 
 
At SPECTRAFORCE, we are committed to maintaining a workplace that ensures fair compensation and wage transparency in adherence with all applicable state and local laws. This position’s starting pay is: $ 60.00/hr.