Clinical BioinformaticistSan Diego, California
The Rady Children's Institute for Genomic Medicine brings together world-class scientists, clinicians and technologists into a shared research infrastructure, one that will enable them to accelerate the translation and implementation of research discoveries for prevention, diagnosis, treatment, and ultimately cures for childhood diseases. The Institute seeks to translate research findings into new clinical tests and treatments to improve patient outcomes, enhance the knowledge in this field among current and future healthcare providers and generate and share data and discoveries with other researchers.
We are looking for a computational-biologist/bioinformaticist with demonstrated experience in a large-scale production setting to deploy, maintain and evolve the bioinformatics framework for a high-throughput, ultra-rapid turnaround time whole-genome sequencing based clinical setting. You will be a part of a team that has built the technology enterprise ground up, using the latest and greatest in infrastructure, data storage and informatics, with a strong focus on automation and integration. The environment is highly cross-functional, with a rich medical research heritage and multitude of collaborations with the biotech industry, academic institutions and federal programs. The end deliverable from your work will tangibly influence the quality of life of the children being seen at children’s hospitals around the country, making your work experience exciting, challenging, rewarding and meaningful. And to top it all, you’ll be located in one the finest cities in the country (San Diego, CA), with a wonderful year-round weather and a multitude of outdoor activity options.
What you’ll do:
- Design, develop and maintain production grade and professional quality bioinformatics workflows for Illumina next-gen sequencing data that will be used to save babies lives in the NICU/PICU and CVICU
- Deploy bioinformatics pipelines locally as well as on the cloud
- Adhere to best software engineering principles
- Debug issues in the bioinformatics eco-system, communicate and document them
- Provide bioinformatics support to upstream laboratory and downstream interpretation teams, and help diagnose problems
- Evaluate NGS analysis tools, benchmark, generate reports and take them to production
- Integrate LIMS with primary (BCL to BAM), secondary (BAM to VCF) and tertiary analyses (VCF to annotated and prioritized report) – both locally as well as on the cloud
- Organize genomic data on local and cloud locations
- Manage genomic data life-cycle (creation to archival and restore)
- Train and support other researchers in the use of bioinformatics pipelines and assist them in the analysis of genomic data
- Develop validation framework for the informatics components
- Perform QC and QA to ensure quality of data getting out the door
- Create and maintain documentation surrounding the analysis framework
- Adhere to compliance requirements (CAP/CLIA)
- Manage multiple competing priorities
- Conversant with generating graphs and presenting metrics and other data in a intelligible manner
- Communicate clearly with a wide variety of stake holders –biologists, geneticists, physicians, lab staff and infrastructure IT staff
- Bachelor's degree in Computer Science, Information Systems, Bioinformatics or Life Sciences, including fields, i.e., Biology, Molecular Biology, Genetics.
- Master’s degree or Ph.D. preferred.
* Minimum demonstrated experience:
Three years of experience:
- analyzing next-gen sequencing data (Illumina whole genomes or whole exomes): BCL to annotated variants
- developing and maintaining pipelines for 24x7 automated bioinformatics analyses
- integrating pipeline with LIMS and other information systems
- working with and understanding of open source NGS tools like bwa, samtools, vcftools, picard, GATK, Freebayes, ANNOVAR, VEP, etc.
- incorporating dbGaP, 1000 genomes, ExAC, Clinvar, OMIM, HGMD, etc
- experience with unix/linux operating system
- software development using any of Python, Perl, Ruby or Bash
- working with git
- working with HPC scheduling systems such as Moab, TORQUE, LSF, OpenGrid Engine, etc.
- A good sense of process engineering and software development life cycle
- Demonstrated experience in:
- WDL or CWL base pipeline development
- CNV and SV calling
- phenotype-genotype integration frameworks
- cloud-based development or analysis
- working in a CAP/CLIA environment
- developing and working with Docker and AWS images