Introduction

Learning Objectives

• How to Access SRA data in GCP's BigQuery
• How to run common queries against SRA metadata in BigQuery
• Different methods for retrieving SRA data in the Cloud
• One approach to assessing reference genome coverage
• How to query SARS-CoV-2 SRA data using precalculated variant calling results in BigQuery

Background Knowledge

• General familiarity with writing SQL queries
  • A google search for SQL basics will reveal a number of decent tutorials
• General familiarity with Next-Generation Sequencing (NGS) data
• General familiarty with variant calling and the VCF files format
  • The VCF specification can be found here

Help Documentation

• General documention on finding and downloading SRA data can be found here
• Documentation on the SRA TAxonomy Analysis Tool (STAT) can be found here
• General documentation on SRA cloud resources can be found here
• Documentation on NCBI's SARS-CoV-2 Variant Calling Pipeline can be found here
• GCP BigQuery documentation can be found here
• Documentation on the SRAToolkit can be found at the associated GitHub page
• minimap2 documentation can be found here
• samtools documentation can be found here
• jq documentation can be found here
• gnuplot documentation can be found here

Other Resources

• The AWS Open Data Program can be found here
• Documentation on GCP Public Datasets can be found here
• AWS Athena documentation can be found here
• The initial publication on STAT can be found here