During my time as a bioinformatician at the UC Davis Genome Center and in the Dubcovsky and Ross-Ibarra labs, I found very few books taught the data skills I relied on most in my day-to-day bioinformatics work. Furthermore, texts didn’t emphasize scientific computing best practices alongside teaching technical skills.
Bioinformatics Data Skills (published by O’Reilly Media in July 2015 and now one of the most popular books in the field) is my book that seeks to fill this role.
You can purchase Bioinformatics Data Skills from an independent bookstore like Powell’s City of Books or Amazon.com .
Reviews
Below are some quotes from reviews of Bioinformatics Data Skills. Other reviews are available at Goodreads (4.3/5 stars, 72 ratings), Amazon (4.6/5 stars, 136 ratings), and O’Reilly (4.8/5 stars, 14 reviews). You can also read the review written by the terrific Molecular Ecologist blog. If you’d like to share your review, tweet it, and ping me at @vsbuffalo .
Have I said lately how wonderful @vsbuffalo’s book is? “#Bioinformatics #Data Skills.” Buy it. For real.
— Sean Leonard (@spleonard1 ), December 2015
I wish this book was available two years ago when I first started my graduate studies - It literally could have saved me a year.
— Gur, review on O’Reilly.com
Superb book for those looking to develop bioinformatics skills. Covers loads of the supporting skills that are generally learnt through years of experience and aren’t obvious in other texts/courses. Should be required reading for any PhD students or lab scientist working with data.
— Simon B, review on O’Reilly.com
I have been programming in a UNIX environment for 26 years, and a leader in bioinformatics since I entered the field in 1998, and was surprised to find that I was able to learn useful tips and tricks in nearly every chapter.
— KATS, review on O’Reilly.com
This is literally “must read” for bioinformaticians. It teaches skills which will always be required, whatever software tools and technologies are around in 10 years.
— Alex Ishkin, review on Goodreads
This is my new “go to” recommendation for people looking to get into the field.
— Philipp, review on Goodreads
Very good book. And 85% of it will be just as relevant in ten years, which is an achievement.
— Endre Bakken Stovner, Biostars
Audience
Bioinformatics Data Skills is an intermediate-level book, aimed at readers with some experience with a scripting language like Python, and very basic Unix (e.g. the Unix filesystem hierarchy, cd, ls, etc.). Bioinformatics Data Skills gives readers a solid Unix foundation in chapters 3 (“Remedial Unix Shell”), 7 (“Unix Data Tools”), and 12 (“Bioinformatics Shell Scripting”, “Writing Pipelines”, and “Parallelizing Tasks”). Readers are also introduced to the R language through learning exploratory data analysis (chapter 8).
Supporting Materials
Bioinformatics Data Skills has over 700 code examples for readers to follow along with. All supporting data and scripts (as well tips, anecdotes, and extended footnotes) are available in my book’s Github repository at github.com/vsbuffalo/bds-files .
Errata
Readers can submit and view errata for Bioinformatics Data Skills on O’Reilly’s website . I’ve also posted some important corrections on the book’s Github repository .