Processing 16S data
Processing 16S data
An informal primer about 16S rRNA amplicon data
About the Book
My goal for this document is to help you understand the theory behind 16S data processing. I want you to be able to do the analysis that makes the most sense for you. There are pipelines that make data analysis easy and simple. I aim to show you how the sausage is made. The entire data collection process, from sample collection to OTU calling, is discussed, with particular emphasis on preparing raw sequencing data for OTU calling and on selection of OTU calling methodology.
- Where this document came from
- What this document is for
- Who this document is for
- What this document is not
Where 16S data comes from
- The 16S gene
- Getting DNA from a sample
- Amplifying the gene
- The amplified DNA is not exactly like the original DNA
- Multiplexing helps evaluate contamination (or other weirdness)
Data processing theory
- Raw data and metadata
- Overview of the processing pipeline
- Details of each step
- An abridged history of the OTU
- Why call OTUs?
- OTU calling is not the same as lineage assignment
- Common and uncommon OTU-calling methods
- File formats
- Existing tools
- Your own tools
- Some early challenges
- Pipeline tutorials
The Leanpub 60 Day 100% Happiness Guarantee
Within 60 days of purchase you can get a 100% refund on any Leanpub purchase, in two clicks.
Now, this is technically risky for us, since you'll have the book or course files either way. But we're so confident in our products and services, and in our authors and readers, that we're happy to offer a full money back guarantee for everything we sell.
You can only find out how good something is by trying it, and because of our 100% money back guarantee there's literally no risk to do so!
So, there's no reason not to click the Add to Cart button, is there?
See full terms...
80% Royalties. Earn $16 on a $20 book.
We pay 80% royalties. That's not a typo: you earn $16 on a $20 sale. If we sell 5000 non-refunded copies of your book or course for $20, you'll earn $80,000.
(Yes, some authors have already earned much more than that on Leanpub.)
In fact, authors have earnedover $12 millionwriting, publishing and selling on Leanpub.
Learn more about writing on Leanpub
Free Updates. DRM Free.
If you buy a Leanpub book, you get free updates for as long as the author updates the book! Many authors use Leanpub to publish their books in-progress, while they are writing them. All readers get free updates, regardless of when they bought the book or how much they paid (including free).
Most Leanpub books are available in PDF (for computers) and EPUB (for phones, tablets and Kindle). The formats that a book includes are shown at the top right corner of this page.
Finally, Leanpub books don't have any DRM copy-protection nonsense, so you can easily read them on any supported device.