Below are publicly available protocols to assist with uploading data to public access repositories.
Below are bioinformatics resources, including workflows developed on commercial platforms such as CLCbio:
NextStrain provides data visualization builds for each state using publicly available datasets. To view state specific builds, please visit the SPHERES NextStrain page.
Example reports summarizing genomic surveillance data for jurisdications are provided below:
Northeast Region SARS-CoV-2 Training
Training covering sequencing methods for SARS-CoV-2, Linux, Terra.bio and data visualization and sharing with public databases.
May 2020 Demystifying Webinar Series-SARS-CoV-2 Resources
Webinar discussing the multitude of resources available for SARS-CoV-2 sequencing and data sharing with an emphasis on resources most applicable to state PHLs.
COVID-19 Genomic Epidemiology Toolkit
From the Office of Advanced Molecular Detection (AMD), this toolkit addresses topics related to the application of genomics to epidemiological investigations and public health responses to SARS-CoV-2.
This documentation covers topics related to SARS-COV-2 and Nextstrain including preparing your data, running and customizing your analysis and data visualization and sharing.
QMS Tools and Resources
CDC and APHL adopted the CLSI 12 QSEs as building blocks for developing a QMS for clinical and public health laboratories performing NGS-based tests.
The National SARS-CoV-2 Strain Surveillance (NS3) program was established to provide baseline surveillance
information as well as information on currently circulating variants of
concern. Guidance documents, FAQs and program contact information can be found
on our NS3 webpage.