Taxa-based filtering in 2017.10?

@jairideout @gregcaporaso I just wanted to confirm that filtering taxa is coming out in the next release 2017.10? I have managed to delay making this tutorial for my current class and an upcoming 2-day workshop in mid Nov. I can hold out another couple of weeks if it will be out soon (as opposed to moving forward with a more complicated tutorial using QIIME1, which some folks in my class are not familiar with). Thank you!!

Hi @jessicalmetcalf, I’m literally working on this today, and I don’t see any issues with it making it into 2017.10. Barring some unforeseen disaster, it’ll be in there.

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@jessicalmetcalf, one question: Can you describe specifically what you’re wanting to filter? I want to make sure that what I’m currently working on will address your needs.

Hi @gregcaporaso, sorry to just jump into your conversation but this topic really appeals to me. For qiime2 users, I think we usually desire to filter out taxa assigned as mitochondria and chloroplasts. Additionally, we may want to exclude taxa that are present in the negative controls and have been identified as contaminating sequences.

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Thanks for these ideas @yanxianl! I think what @gregcaporaso and @Nicholas_Bokulich are working on will address those use-cases.

Yes, that’s correct.

One note though: we won’t be providing information on taxa/sequences that are likely to be contaminants, but if you have that information, the functionality being added in 2017.10 will allow you to filter using it.

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QIIME 2 2017.10 was just released! There are some new methods in q2-taxa and a brand new section in the Filtering Tutorial explaining how to filter certain taxa from your data.

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