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Bioinformatics Engineer- Remote

Posted 22 days ago

We have an amazing opportunity for a Bioinformatics Engineer, apply today if you have 2-4 years with:
  • BS or MS with 2 to 3 years of experiences in computer sciences, software engineering or data sciences areas.
  • Strong programming skills in a variety of languages, such as Python (strongly preferred), R, and Perl, and familiarity with the command line interface (CLI).
  • Expertise in bioinformatics and genomics, including knowledge of commonly used tools and pipelines for processing and analyzing genomic data.
  • Experience with Nextflow or other workflow management systems (e.g., CWL, WDL), including building and deploying bioinformatics pipelines.
  • Familiarity with common bioinformatics file formats, such as FASTQ, BAM, and VCF, and experience with data wrangling and manipulation.
Strong pluses:
  • Experience with cloud infrastructure providers such as AWS, Google Cloud, or Microsoft Azure, and familiarity with deploying and managing bioinformatics pipelines in the cloud.
  • Knowledge of DevOps practices, including continuous integration, continuous deployment, and automated testing, and experience with version control systems such as Git.
  • Experience with software validation and quality control, and familiarity with regulatory and quality standards such as CLIA, CAP, and HIPAA.
  • Excellent communication and collaboration skills, with the ability to work effectively in a remote or distributed team environment.

  • Use Nextflow to build a bioinformatics pipeline that takes FASTQ files as input and processes them using bioinformatic tools.
  • Integrate common bioinformatic tools such as BWA-MEM, GATK, or FreeBayes into the pipeline.
  • Write Python/R scripts to process, summarize, and visualize outputs created by other tools.
  • Ensure that the pipeline is modular and flexible, with the ability to add or remove tools as needed.
  • Implement quality control measures such as FastQC to ensure that the input data is of high quality and meets the required standards.
  • Implement data preprocessing steps such as trimming, filtering, and adapter removal to prepare the data for downstream analysis.
  • Implement variant calling and annotation tools to identify and annotate variants in the data.
  • Implement filtering and prioritization steps to identify clinically relevant variants and exclude non-pathogenic variants.
  • Implement a reporting system to generate a clinic-ready report that summarizes the findings and provides actionable recommendations.
  • Ensure that the pipeline is reproducible, with the ability to generate the same results from the same input data.
  • Provide clear and concise documentation on how to use and manage the pipeline, including instructions on how to install and configure the necessary software and tools.???????

Candidates will be responsible for following the client's COVID-19 protocols. Please refer to your MATRIX representative for specifics.

About Us

At MATRIX, we expertly match talented professionals with job opportunities to elevate careers. Since 1983, we have placed thousands of professionals at innovative clients across every industry ranging from small startups to Fortune 50 companies. It’s why we’re consistently in the top 25 of all U.S. IT staffing firms and why our consultants rate us well above the industry average, earning us ClearlyRated's Best of Staffing awards year after year. People come to us for a job, and stay with us because of our top-notch consultant care.

MATRIX is and Equal Employment Opportunity employer including disability and veteran and provides reasonable accommodations for all qualified individuals.  Supporting medical or religious documentation will be required where applicable. If you are a qualified individual you may request a reasonable accommodation under the American Disability Act (ADA). If you are a person with a disability needing assistance applying, or at any point in the hiring process, please email us at To ensure a quick response to your request, please use the words “Accommodation request” as the subject line of your email.

For hourly W2 contract roles MATRIX offers a highly competitive benefit package including Medical, Dental, Vision, Life, Disability, HSA, and 401(k) with pre and post-tax options.  Please see for more information.

For direct hire placement with our clients, benefits would be offered in accordance with that particular client’s offerings. This may include PTO, Medical, Dental, Vision, 401K and other pre and post-tax options.