Genomics cloud computing book recommendation: Genomics in the Cloud Using Docker, GATK, and WDL in Terra

created at 06-04-2022 views: 6

Recommend a book to friends who are learning genomic cloud computing, "Genomics in the Cloud: Using Docker, GATK, and WDL in Terra", the author is the GATK community administrator, published in 2020, it is relatively new.

Genomics in the Cloud Using Docker, GATK, and WDL in Terra

Github address: genomics-in-the-cloud

This book covers:

  • Basic genomics and computational technology background
  • Basic cloud computing operations
  • Getting started with GATK, and the three main GATK best practice pipelines
  • Automate analysis using scripted workflows using WDL and Cromwell
  • Scale workflow execution in the cloud, including parallelization and cost optimization
  • Interactive analysis in the cloud using Jupyter notebooks
  • Secure collaboration and computational repeatability using Terra

The book is very thick, and it spends a lot of time introducing Broad's own products, but we basically don't use its cloud platform Terra, and the layout is very poor, which is the shortcoming of this book. Also, the book is written for the human genome, so its scope is limited. However, it is a good choice to select some chapters selectively, after all, there are too few books in this area.

created at:06-04-2022
edited at: 06-04-2022: