Bioinformatics Associate II (Hybrid)

Details for the position are as follows: • Rate: $45-64.85 an hour • Location: South San Fransico, CA - Hybrid role MUST be able to come onsite 1 day a week • 6 month contract to start with the possibility of extension or conversion depending on performance and business needs. Job Description: • Lead the development and optimization of bioinformatics pipelines and analyze NGS datasets in close collaboration 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. • Develop, automate, and maintain scalable, reproducible pipelines for RNA-seq, WGS/WES, scRNA-seq, and other NGS data across HPC and/or cloud environments • Perform advanced analyses including variant calling, differential expression, transcriptomic/epigenomic analysis, pathway enrichment, and genomic annotation • Conduct quality control for FASTQ, BAM/CRAM, VCF, and related data formats • Write efficient, well-documented Python or R code; build custom tools for data integration, visualization, and analysis • Implement, evaluate, and adapt bioinformatics tools and algorithms, integrating open-source resources as needed • Collaborate closely with wet-lab scientists to align analyses with experimental design and interpret results • Troubleshoot pipeline failures, data issues, and performance bottlenecks while ensuring data integrity and reproducibility • Prepare clear reports, visualizations, and presentations; maintain thorough documentation of workflows and code • Stay current with emerging NGS technologies, tools, and computational methods Required Skills: • Master’s degree with 5+ years of hands on experience within bioinformatics/comp genomics required • Python or R programming experience required • Experience with NGS datasets and implementing standard workflows required • Experience with Public genomic datasets (NCBI / Ensembl / UCSC / GTEx / TCGA) required • Experience with at least one of the following: STAR / BWA / Bowtie / GATK / Samtools / bcftools required • Experience with at least one of the following: DESeq2 / EdgeR / Seurat / scanpy required • Hybrid role MUST be able to come onsite 1 day a week in South San Fransico, CA. Preferred qualifications: • 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