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Workshop goals

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Workshop

0 Set-up

1 NCBI Pathogen Detection

• 1 Introduction to Pathogen Detection
• 1a Isolates Browser
• 1b E. coli resistant to meropenem-AST Browser
• 1c MicroBIGG-E
  • genes_on_contig
• Accessing NCBI Pathogen Detection data using BigQuery in Google Cloud
  • Get started with 1d BigQuery for Pathogen Detection
  • 1e BigQuery Exercises
• Useful links for more information

2 Datasets

• 2.1 NCBI Datasets: an overview

3 SRA

• 3.1 Searching SRA via the Web
• 3.2 Searching SRA via GCP BigQuery
• 3.3 Using SRAToolkit to retrieve Data
• 3.4 Examining Assemblies from SRA Normalized and Lite Format Files

4 Some Useful Links

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Don't have a cloud account?

NIH Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative has launched a new NIH Cloud Lab program that lets you experiment with using cloud for your research. You can request a GCP or AWS account, and will receive $500 and three months, in addition to access to biomedical tutorials that walk you through common cloud-based research use cases. This is available to intramural researchers currently but expect it to be ready for extramural researchers in the coming months. Learn more via this link- https://cloud.nih.gov/resources/cloudlab/

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Has this been useful?

Please let us know at [email protected] if this has been useful and if you're using any of these resources in your work and especially if you use these resources in your publications.

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Post-workshop updates

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