Genomics in the Cloud: Using Docker, GATK, and WDL in Terra 1st Edition

*Review update at the bottom*I am halfway into reading this book. There are many things I like and a handful I don't. So, let me start with the good stuff.- I like the concise and well balanced introduction, to both computation and genomics, that lays a good ground for the practical hands-on exercises you will encounter in the book. This will greatly help those new to the field of computational genomics and bioinformatics and to those who would like to brush up the basics.- I like the step-by-step instructions for the hands-on genomics data analysis exercises that will help you get started with comfortably working in the google cloud.- I like the right dose of humor by the authors that will make reading joyful and personalized for the reader.- I like the presence of best practice guidelines all in one place. Sometimes, it can be overwhelming to keep up with the documentation online on the GATK website and I see this book as a handy reference point.- I like that if you are a routine GATK user, you can expect to learn tips/tools (that you were unaware of) that could help you improve your genomic data analysis workflows.Coming to what I don't like.- I don't like the poor quality of figures, specifically IGV screen shot's which can give you a hard time interpreting the results if you are simply reading the book and not doing hands-on exercises.- I do not like the release timing of the book. I think it would have better helped the community if it had released post the release of public version of DRAGEN-GATK pipeline. I say this because with the release of public version of DRAGEN-GATK pipeline some parts of this book will be obsolete. I don't know if the authors are planning a new version of the book soon after the release of public version of DRAGEN-GATK pipeline. If yes, that would be really helpful for the community.I am giving 4 stars for how incredibly helpful I am finding this book to learn new skills that I previously didn't have which I am finding helpful in improving the quality of genomic data analysis. A resource like this is needed but with frequent updates as technologies and methods of analysis evolve. So, I recommend buying the book and if you do I recommend following Geraldine's twitter work account where she posts updates, if any, to any sections of this book.*Update 11/21/2020*The author, Geraldine, was very kind to read my review and address the concerns I raised. She plans to release a color PDF with the figures and IGV screenshots that users can self-print. Also, there will be necessary updates made to the book soon after the release of public version of DRAGEN-GATK workflow for germline variant detection. So, make sure you watch out for updates. Also, I forgot to mention earlier that she sends out stickers for GATK, WDL, Terra and/or Cromwell if you buy the book and upload a pic on twitter.

If you are a bioinformatician exploring how to scale, standardize or deploy your pipelines in a cloud environment this book is really a must have.Even if you are a beginner this book will take you from basic genomic concepts to advanced skills in a very friendly and clear way.Geraldine is one of the best communicators regarding Genomics in the cloud and her way of teaching and helping others to understand these tools transpires trough this book.I have been using this book to understand new techniques and as the Genomic product owner at my current position I can say that it has been an extraordinary tool.This is the perfect gift for the Bioinformatician in your life ;)

Terrible graphics quality. Even BW graphics have a palatable quality, but no...But that's not author specific really, all ORielly books suffer from this. Valiant effort by the team at Broad Inst tho...

My son is earning his PhD in Biology and asked for this book. I waited until he read to review. He is one of those readers who is aware of the different publications of a classic and wants a particular one or that is aware of author in cases like this to be interested in the first place. He enjoyed the book and gives his stamp of approval.

Becoming a skilled practitioner of cloud-based bioinformatics is within reach, no matter where you live. Armed with this book, I recently led a global book club on Zoom with 35+ members that spanned ten time zones. We covered one chapter per week and finished in 14 weeks. The book is kind to computer scientists and biologists/genomicists alike, providing respective background chapters—including an overview of the promises and challenges of using big data in research—that ease you into the material. Making use of free credits on the Google Cloud Platform (GCP), the authors lead you step-by-step to create an account, launch cloud-based virtual machines on GCP, and run Docker-based images of GATK. After covering germline and somatic variant discovery using GATK with well-illustrated examples (and a downloadable color figure booklet), you will learn how to automate workflows with tools like Cromwell and Jupyter notebooks. The surprise at the end of the book (spoiler alert!) is Terra. This data platform is a tour de force that automates much of the drudgery found in bioinformatics. The book concludes where it began: illustrating the benefits of reproducible research through a case study. The writing style is clear and playful—once, I left a coffee stain in the book when I completely lost it. Highly recommended. I received this book as a birthday present from my mother. Although she does not own a computer, I will print this review and mail it to her. Thank you, Mom!

This book is a must if you are learning about and conducting Genomic research. Rich with explanations, examples, and how-tos using the preeminent tools.. As important, it is accessible to all, from those simply wanting to learn more - to experienced researchers. The two authors are well known and respected - it shows.

After two years of waiting, I received a book printed in black and white, with pages written in shades of gray and with painful graphics (imagine a IGV shot in greys tones). A real disappointment. It looks as if it had been printed with little toner or ink, with a painful and unacceptable end result for a book at this cost. I return it on the go. I have been told that the ebook has color images. The book I have received only has color on the cover. Logically, it is not a problem of the authors, but of the publisher or the printer. I know the content is valuable, but not in this condition.

The first four chapters are very good to initiate us to Cloud computing. However the latter chapter are focused on human genomics and on the tools developed at the Broad institute. There is much more in genomics that human genomics and the title should include "Include". Not a single word on bacterial genomics, eukaryotic genomics or metagenomics. On the positive side the book is very well written and very easy to follow.