Make a modernized (i.e., Python > 3.5) QIIME friendly to fungal microbiomes

[ajpowel]

Hello,

I am a fungal researcher, & would very much like to use QIIME to analyze my datasets, however, it seems best-suited to handing bacterial microbiomes, & performs relatively poorly w/ fungal classification analyses. For instance, some of my collaborators have mentioned that fungal OTUs have been inappropriately "split." Perhaps we could help with these issues...? Many thanks & all the best for considering. AJP

[jairideout]

QIIME is not specific to bacterial microbiome analysis. Recent versions of QIIME 1 ship with Greengenes, a 16S reference database, but you can use different reference databases for other types of analyses. There's a fungal ITS tutorial that illustrates how to do this. See the resources page for available reference databases that are QIIME-compatible, and you can always create your own reference database if those aren't suitable.

Besides swapping out your reference database, other steps in your analyses may need to be changed depending on your marker gene. For example, with ITS data it is difficult to create a meaningful multiple sequence alignment, so those steps in the analysis would need to change vs. what you'd do in a 16S analysis (the fungal ITS tutorial covers this in more detail).

If there are specific fungal analysis methods that are missing and would be useful to have in QIIME, I recommend developing a QIIME 2 plugin, that way the methods are available to other QIIME 2 users. We are no longer adding new features to QIIME 1.

Thanks!

[ajpowel]

Hello,

Is there a pip installation for QIIME 2? I'm looking at the documentation, & nothing leaps out. Many thanks!

Best,

AJP

On 10 April 2017 at 16:09, Jai Ram Rideout notifications@github.com wrote:

QIIME is not specific to bacterial microbiome analysis. Recent versions of QIIME 1 ship with Greengenes, a 16S reference database, but you can use different reference databases for other types of analyses. There's a fungal ITS tutorial http://qiime.org/tutorials/fungal_its_analysis.html that illustrates how to do this. See the resources page http://qiime.org/home_static/dataFiles.html for available reference databases that are QIIME-compatible, and you can always create your own reference database if those aren't suitable.

Besides swapping out your reference database, other steps in your analyses may need to be changed depending on your marker gene. For example, with ITS data it is difficult to create a meaningful multiple sequence alignment, so those steps in the analysis would need to change vs. what you'd do in a 16S analysis (the fungal ITS tutorial covers this in more detail).

If there are specific fungal analysis methods that are missing and would be useful to have in QIIME, I recommend developing a QIIME 2 plugin https://docs.qiime2.org/2017.2/plugins/developing/, that way the methods are available to other QIIME 2 users. We are no longer adding new features to QIIME 1.

Thanks!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biocore/qiime/issues/2189#issuecomment-293093546, or mute the thread https://github.com/notifications/unsubscribe-auth/APG2vI6fAfkjPDNGLp0OYFek9FqmL23eks5ruqiLgaJpZM4M5F-K .

-- Regards, AJP

[gregcaporaso]

@ajpowel, can you please post your question to the QIIME 2 Forum? We provide technical support for QIIME 2 there. Thanks!