2021 Project: J Michael Consulting

Implementation of cloud-hosted bioinformatics infrastructure to facilitate standardization, quality and submission of SARS-CoV-2 and other pathogen sequence data to public repositories

What to know

J Michael Consulting developed a proof-of-concept bioinformatics platform for use by state and local public health partners. This project sought to automate the submission of quality, curated sequenced data directly to the National Center for Biotechnology Information (NCBI) and CDC databases for SARS-CoV-2. These systems could establish the technological foundations of a national network to fully combine next-generation sequencing data into public health surveillance, monitoring, and research efforts.

Decorative image with words "2021" and "SARS-CoV-2"

New SARS-CoV-2 dashboards and websites

This project established a cloud-hosted portal called Partner Communication Engine (PCE) for the management of communications between partner laboratories, the National Center for Biotechnology Information (NCBI), and CDC. PCE supports data sharing functionality that allows for efficient and secure exchange of sequence data.

New and improved sequencing software tools

This project built the MiSeq Sequencing Interface platform that integrates with Utah's Cecret Bioinformatics pipeline.

The platform:

  • Manages quality control for genomic data through the sequencing and bioinformatic processes based on PHA4GE standards.
  • Visualizes genetic results by integrating with Nextstrain.
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Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)