staph-b/southeast-region

Scripts, pipelines, and training materials for the AMD Southeast Region

Bioinformatics Resources for the AMD Southeast Region

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 and Workforce Development (WFD) Lead)
• Louisiana
• Mississippi
• Puerto Rico
• Tennessee
• U.S. Virgin Islands

HiPerGator Resources

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 150 CPUs to run analyses. Additionally, each user has access to a local, private instance of Galaxy, maintained by UF's Research Computing staff. We currently are not providing additional trainings related to Galaxy. For and training or guidance requests please email [email protected]

Getting Started

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.

Training Materials

Trainings

• Intro to Linux 101 (12/09/2022)
• BaseSpace Command Line Interface (01/17/2023)
• HPC and HiPerGator (HPG) (12/08/2022)
• Analysis Options (01/05/2023)
• Tree annotations using R
• Office Hour Presentations
• SARS-CoV-2 Data Submissions Training Series, Part 1-5 (09/15/2021)
  

Meetings

• AMD SE Region Check-in Call (02/02/2023)

To download the slides for past trainings, please visit trainings. Recordings of these videos can be found on the Southeast Region Playlist within the StaPH-B youtube channel link

Additional Resources

SARS-CoV-2 Sequencing

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.

Nextstrain

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 link below to see the latest genomic epidemiology of SARS-CoV-2 in your state, and track variants of concern.

https://nextstrain.org/groups/spheres/ncov/alabama
https://nextstrain.org/groups/spheres/ncov/florida
https://nextstrain.org/groups/spheres/ncov/georgia
https://nextstrain.org/groups/spheres/ncov/louisiana
https://nextstrain.org/groups/spheres/ncov/mississippi
https://nextstrain.org/groups/spheres/ncov/puerto-rico
https://nextstrain.org/groups/spheres/ncov/tennessee
https://nextstrain.org/groups/spheres/ncov/us-virgin-islands

Training and Other Resources for SARS-CoV-2

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/

Relevant Links

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/

Contact your BRR/co-WFD Lead

Molly Mitchell, PhD
Bioinformatics Supervisor
Florida Bureau of Public Health Laboratories
Florida Department of Health
[email protected]

Nikhil Yengala Reddy, MS
Bioinformatician
Florida Bureau of Public Health Laboratories
Florida Department of Health
[email protected]

Contact your co-WFD Lead

Tonia Parrott, PhD, HCLD (ABB)
Georgia Public Health Laboratory
Georgia Department of Public Health
[email protected]

Arunachalam Ramaiah, MS, PhD
Georgia Public Health Laboratory
Georgia Department of Public Health
[email protected]

Tatyana Kiryutina, MS
Georgia Public Health Laboratory
Georgia Department of Public Health
[email protected]