This is the place where you can find all updated bioinformatics resources for the Southeast Region.
Southeast Region members:
- Alabama
- Georgia (Workforce Development (WFD) Lead)
- Florida (Bioinformatics Regional Resource (BRR) Lead)
- Louisiana
- Mississippi
- Puerto Rico
- Tennessee
All Southeast region members have free access to shared computational resources on the high-performance computing (HPC) cluster at the University of Florida, known as "HiPerGator". Each state has their own storage allocation and has access to 64 CPUs to run analyses. Additionally, each user has access to a local instance of Galaxy, maintained by UF's Research Computing staff.
To request a HiPerGator account, please follow these instructions.
If this is your first time using HiPerGator (or any HPC), I highly recommend watching these short training videos.
Please see the UFRC Help and Documentation wiki page for detailed information about HiPerGator and submitting jobs.
All materials related to HiPerGator can be found here.
To access Galaxy, visit https://galaxy.rc.ufl.edu/login.
All materials related to Galaxy, provided by the Southeast BRR, can be found here.
- Southeast Bioinformatics Regional Resources (12/06/2019)
- Intro to Linux (06/19/2020)
- BaseSpace Command Line Interface (07/20/2020)
To download the slides and/or recordings for past webinars, please visit here.
Please visit https://github.com/CDCgov/SARS-CoV-2_Sequencing to find up-to-date sequencing protocols, bioinformatics pipelines/methods, and additional information related to data submission and standards.
For more information on (or to join) the SPHERES (SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance) national consortium, please visit https://www.cdc.gov/coronavirus/2019-ncov/covid-data/spheres.html.
Please visit https://nextstrain.org/community/SESchmedes/sarscov2-southeast-usa/southeast to view the Nextstrain build focused on the AMD Southeast Region. This build will be updated biweekly. You can drag and drop a .csv file with your own metadata to view additional information pertaining to your samples. The added metadata does not leave the browser.
Additionally, SPHERES maintains state-level builds for all 50 states at https://nextstrain.org/groups/spheres. Click on your state to see the latest genomic epidemiology of SARS-CoV-2 in your state, and track variants of concern.
CDC's COVID-19 Genomic Epidemiology Toolkit - A module-based training toolkit for public health officials to understand the application of genomics to epidemiologic investigations and public health response to SARS-CoV-2. https://www.cdc.gov/amd/training/covid-19-gen-epi-toolkit.html
SARS-CoV-lineages - Up-to-date SARS-CoV-2 lineages, global variant reports, and a web-browser application (Pangolin) to determine lineage from fasta files. https://cov-lineages.org/
CDC's Advanced Molecular Detection (AMD) program - https://www.cdc.gov/amd/who-we-are/index.html
StaPH-B (State Public Health Bioinformatics) Group - http://www.staphb.org/
Sarah Schmedes, PhD
Florida Bureau of Public Health Laboratories
Florida Department of Health
sarah.schmedes@flhealth.gov
Tonia Parrott, PhD
Georgia Public Health Laboratory
Georgia Department of Public Health
Tonia.Parrott@dph.ga.gov