Software Guidance & Assistance, Inc. (SGA, Inc.) · 3 days ago
Bioinformatics Associate II
South San Francisco, CA
Full-time
Onsite
Senior Level
$62/hr - $67/hr
5+ years expSoftware Guidance & Assistance, Inc. is searching for a Bioinformatics Associate II for a contract assignment with one of their premier Pharmaceutical clients. The role involves leading the development and optimization of bioinformatics pipelines, analyzing NGS datasets, and collaborating with cross-functional research teams.
Information TechnologyStaffing Agency
Hiring Manager
Priti Arora
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
Qualification
Required
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
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
Company
Software Guidance & Assistance, Inc. (SGA, Inc.)
SGA is the technology and resource solutions provider driven to stand out. We are a certified women-owned business.
201-500 employees
H1B Sponsorship
Software Guidance & Assistance, Inc. (SGA, Inc.) has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (13)
2024 (12)
2023 (19)
2022 (25)
2021 (41)
2020 (44)
Funding
Current Stage
Growth StageLeadership Team
Peter Taylor
CEO
Andrew Gallagher - CCWP
Senior Vice President - Strategic Partnerships
Company data provided by crunchbase