4. Some Useful Links

NCBI Documentation

Pathogen Detection

• NCBI Pathogen Detection home page
• NCBI Pathogen Detection documentation
• NCBI Pathogen Detection training videos
• NCBI Pathogen Detection HowTo guides - Short PDF/Powerpoints with screenshots showing how to do some common tasks with our web interfaces.
• Pathogen Detection Resources at Google Cloud - Includes many example queries for different tables and also how to download contig and protein sequences.

Datasets

NCBI Datasets main resources

• NCBI Datasets homepage: https://www.ncbi.nlm.nih.gov/datasets/
• Github: https://github.com/ncbi/datasets
• Download and installation instructions: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/

Tutorials, how-to guides and past workshops

• How-to guides (short, one-line CLI tasks):
  https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/
• Tutorials (multi-task, longer tutorials, mostly based on feedback or questions we get from users): https://www.ncbi.nlm.nih.gov/datasets/docs/v2/tutorials/
• Past training sessions and workshops (Jupyter notebooks used in previous datasets training events): https://github.com/ncbi/datasets/tree/master/training

SRA

• SRA Home Page
• SRA Archive Documentation
• SRA in the Cloud Documentation
• SRA Toolkit Download Instructions
• SRA Data Locator

Cloud Service Provider (CSP) Documentation

GCP

• BigQuery
  • There's a Gemini link () conveniently located in top bar of the Google BigQuery page, and that can be useful for asking questions and for help with SQL.
  • BigQuery SQL - An introduction to the specific differences in BigQuery SQL from other SQL dialects.
  • BigQuery syntax - This page has some examples of queries

AWS

Other Web Resources that may be useful in leveraging Pathogen Detection/Datasets/SRA Resources