NCBI ASHG Workshop 2021
Enhanced Search Capabilities and Ease of Use of NCBI SRA Data on the Cloud
This workshop will introduce you to powerful metadata searches for the Sequence Read Archive (SRA) by using interactive metadata queries in the cloud. This service expands the search tools available for SRA and saves time by finding exactly the data you want more quickly than ever before. We will discuss metadata searches in AWS and GCP using common database query methods and demonstrate how to use the metadata tables for searching.
We’ll run through these hands-on exercises:
1.) finding sequence data based on k-mer searches for specific taxonomic IDs and
2.) filtering runs to find exactly what you want.
We will also provide demonstrations and examples to help you better understand how to build your own searches and find the data you want.
We will be using Structured Query Language (SQL) to do these searches but no prior SQL experience is required. By the end of this seminar you will know how to run cloud metadata queries to find SRA data based on parameters that interest you.
Instructors
Adam Stine, M.S.
Adelaide Rhodes, Ph.D.
Agenda
Lecture: Getting Started with GCP on BigQuery
How to Log In
Hands-On Activity/Demo in GCP BigQuery
Hands-On Activity/Demo in AWS Athena
Join the Hands-On Portion of the Tutorial Here!
Please be advised that in many cases the permissions have been set to allow Notebooks to run on our servers. Some additional programs may need to be loaded to help the notebooks run if they are transferred elsewhere. Also, permissions to make queries to BigQuery and AWS require credentials that can be set up by your institution.
The Live Link is Deprecated now that the Workshop has Ended.
Here’s a link to the live workshop
The video link isonly available with ASHG login for attendees who want to review the presentations.
Additional Resources From the Workshop
PDF Version of Slides Explaining Console Based Set Up of GCP BigQuery
PDF Version of Slides Explaining Console Based Set Up of AWS Athena
Websites
• Interactive SQL Primer at KhanAcademy - Khan Academy Intro to SQL and Databases
Tutorial Videos
• SRA Metadata in the Google BigQuery
• SRA Metadata in Amazon Athena
