Hi everyone i just had a quick question. I see a lot of authors still use QIIME 1. Is there any benefit of using one over the other?
Is QIIME2 better in anyway than QIIME1?
Best wishes.
Hi @Mantella86,
I personally don't see many people still using QIIME1, but I may been biased on that!
However, to give you my opinion, I see them as tools to create pipelines, there may be tools available for both pipelines and tools available only in one or the other.
All the methods performed by scripts within the QIIME1 pipelines are still valid (as far I know ...), some implementation may be updated but I don't think any reviewer may say they are not usable.
That said, any tools you could use is available as stand-alone, and as long as you have an expertise on scripting, you could import most of their results into either QIIME1 or QIIME2.
This is, I think, where the differences arises! To use QIIME1 you probably need more developed scripting skills, especially if you like to import into it result obtained with newest tools (which were not available when QIIME2 was developed ... keep in mind it is no longer mantained so you may not even be able to install it into newest computers). As opposite, QIIME2 is a lots easier to install and work with.
Hence, if you have an old machine dedicated to QIIME1 and already-made scripts you know works well, you may still keep using it. If you have just recently entered in this research filed, working with QIIME2 is simply easier.
Most of the times, the question is on using different approaches, such as AVSs identification (more recent approach ) or OTUs clustering (historically the first used to analyse the data) ... But you will find both way available in QIIME2, so I would not use QIIME1 only because you prefer to cluster the sequences into OTUs rather than denoise them into ASVs.
Sorry, this was just a disorganised collection of thought on our question, which, for a short answer, I think is really "dependant on your context".
Hope it helps
Luca
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.