Qiime2 on Windows


I am recently assigned to a project that uses QIIME and i was assigned to a lab team that has been using qiime for a long time. However, all of them runs qiime on a mac and none of them has experience with using qiime on windows. Since i am a comp sci major, i have experience using virtualbox throughout my college years. Do you think if i work with qiime on windows i will run into difficulties with my other lab members being the only one using windows?


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Does qiime2 run better on windows or Mac?

I read that windows is only currently supported by using virtual box. However i was wondering if they will run differently on a mac.


Yes, our lab runs almost exclusively macs, the people with windows usually have to run w/ virtual box. It’s cumbersome, but you’re paying for the apple tax, but you can also partition and run it in linux (e.g., ubuntu/arch linux). I would probably recommend running it in linux if you’re avoiding the mac.

edit: An altnerative would be if your institution has a cluster, it would be easy to run on there.


Hi Victoria_Alexandra,
If you have Windows 10, you can install Ubuntu (I mean Linux Subsystem for Windows) on it and then install qiime2 into it as part of the Windows. Basically, you will have a separate window with a new system and you can run qiime2 there.

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