Frequent Questions and "Best of the QIIME 2 Forum"

The following is a list of frequently asked questions on the forum, with answers, to serve as a point of reference for forum users to quickly find answers, or for forum users and moderators to use as a reference when helping others.

Note: some of these listings are collapsed lists. If you see an arrow next to a title, click the title to expand the list of topic titles related to that subject. :arrow_forward:


DADA2 Error Messages + FAQs (click to see titles)
Importing and Demultiplexing FASTQ data (click to see titles)
Various Taxonomy Classification Topics (click to see titles)
Understanding reference databases and taxonomy (click to see titles)
interpreting PERMANOVA (click to see titles)
Beta diversity and PCoA (click to see titles)
Interpreting ANCOM (click to see titles)

:rocket: :fireworks: :fire: Super helpful list of all alpha and beta diversity metrics :rocket: :fireworks: :fire:

“Best of the QIIME 2 Forum”

These topics are discussions of general interest to forum users on diverse, popular topics. These are similar to the FAQs, in that they should be of broad and general interest, but these instead provide in-depth information on specific topics, and ideally bring in voices from many different forum users.

This is just an initial collection and I hope it will grow. Please post in this topic if you want to nominate any other topics that fit these criteria and are not already listed, all are welcome to contribute! And if you find any nominated topics helpful, please “like” the nomination as well as your favorite post in that topic, to help guide others toward useful discussions and solutions. :heart:

Where/how to publicly deposit sequence data? (click to see titles)
Longitudinal Analysis

p.s., One very notable exclusion from the “best of the forum” list is the various topics in the “community contributions” section of the forum. This is intentional because — in my mind — those are ALL the cream of the crop of the forum. So to clarify, this topic is intended more to highlight the most informative and faqs from among the other forum categories.


DADA2 is not the only way to merge and clean sequences, i think this should be here: