Switching over from QIIME 1 to QIIME 2

Hi QIIME community!

I am really interested to hear your opinions on switching from QIIME 1 to QIIME 2. I am a graduate student and have to rerun my analyses. I am very tempted to switch from QIIME 1 to QIIME 2 due to its ease of use (i.e. the ability to manipulate tables rather than having to regenerate new tables/graphs) as well as the recording function within QIIME 2. What are your thoughts and reservations about switching over?

(As a note I have been learning to code using QIIME 1 and not a highly skilled coder; so if QIIME 2 is radically different than QIIME 1 in terms of coding and scripts please let me know)

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Hello Alexis!

As somebody that has recently made the switch myself (partially thanks to your suggestion), I would say that it is quite intuitive to learn QIIME 2 and transition over from QIIME 1. The coding is slightly different, but not anything that you wouldn’t be able to get a handle of very quickly, especially with the extensive tutorials and guides on how to use the plugins that natively come with QIIME 2.

My main excitement for using QIIME 2 comes from the greatly improved visualizations, and the provenance information that you get from the files you generate. Furthermore, it would be wonderful to get used to QIIME 2 now so that you are more prepared for any future analyses that will most likely be on this platform.

I hope that helps!

Sirtaj Singh


Thanks for the discussion @abrown17 and @Sirtaj-Singh! This forum topic may also be of interest: Should I be using QIIME 2 while it’s in alpha?

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