Workshop: Learn the Best Way to Find Data in NIH’s Sequence Read Archive (SRA) On the Cloud

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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 some 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. We will be using Structured Query Language (SQL) to do these searches but no prior SQL experience is required. By the end of this workshop you will know how to run cloud metadata queries to find SRA data based on parameters that are of interest to you.

Adelaide Rhodes

Cloud Strategist

National Center for Biotechnology Information

I have a Ph.D. in Zoology from NCSU and an M.S. in Biotechnology/Bioinformatics from Johns Hopkins where I honed my skills analyzing "big data” at the molecular, organismal and ecological scale. As a bioinformatician, strategic consultant and now at the National Center for Biotechnology Information, I have assisted dozens of university and government researchers to analyze cancer, crop science, bacteria, virus and plant genomes, transcriptomes and disease variant data sets. I specialize in helping researchers develop pipelines for data-driven discovery on HPC and commercial cloud computing resources (AWS and GCP) and provide consultation on ML and AI projects in the cloud.

Adam Stine

Sequence Read Archive Curator

National Center for Biotechnology Information

Adam has worked as a curator with the SRA for over 10 years. In that time he has helped submitters understand and complete the submission process, worked with sequencing centers to establish automated data submission pipelines, served on working groups for large NIH sequencing projects, and helped with the recent submission interface redesign. Adam also helped design the process of submitting metadata and accessing files in cloud storage and has taught workshops on searching for and using high throughput sequencing data on commercial cloud platforms.


Live Workshop Event
09/15/2021 at 12:00 PM (EDT)  |  Recorded On: 09/16/2021
09/15/2021 at 12:00 PM (EDT)  |  Recorded On: 09/16/2021