Bioinformatics Analyst

Direct W2 contractors only! No 3rd party agencies! No Visa sponsorship available! This is a hybrid (South San Francisco) or remote position based in the Pacific Time Zone or another US-friendly time zone. The initial contract length will be for 6 months. Client is looking for a motivated Bioinformatics Analyst to implement and operate analytical pipelines for long-read sequencing data. This work will support the Program’s goal of increasing the diversity of genetic datasets available for research. Key responsibilities include establishing and running workflows for short and long-read sequencing data and methylation data as well as performing general bioinformatics tasks. The successful candidate will handle day-to-day data ingestion, quality control (QC), and variant calling and methylation data. This role is highly collaborative, requiring regular coordination with international teams to ensure data flows smoothly and results are accurately reported. Responsibilities: Pipeline Implementation: Set up and maintain scalable bioinformatics pipelines for Oxford Nanopore (ONT) long-read WGS and methylation data. Data Operations: Execute workflows for data processing and interpretation. Manage the intake of raw sequencing and methylation data, perform QC checks at multiple stages, and flag anomalies in preliminary results. Documentation: Maintain clear documentation of pipeline runs, QC metrics, and code updates via git. Operational Collaboration: Serve as the technical point of contact for data tasks, coordinating data transfers and status updates with global collaborators, including attending meetings with Africa-based teams (East Africa Time Zone). Skills required: Education: Masters or undergraduate degree in Bioinformatics, Computational Biology, or a related field, with 2+ years of direct, hands-on experience in bioinformatics. Technical Skills: Proficiency in Python and shell scripting (Bash). Experience with high-performance computing (HPC) or cloud environments (AWS). Bioinformatics Experience: Hands-on experience building and running Next-Generation Sequencing (NGS) bioinformatics pipelines (e.g., Nextflow, Snakemake) and direct experience working with human Whole Genome Sequencing (WGS) data Oxford Nanopore (ONT) . Competency with git for code and documentation tracking. Genomics Knowledge: Knowledge on T2T reference standards and pangenome graphs is a plus. General Skills: Strong communication skills for coordinating with global collaborators across different time zones. Proactive mindset with the ability to work independently on technical tasks while following project guidelines.