Running gneiss without using qiime

Hi,

I’m trying to incorporate the gneiss python library (https://github.com/biocore/gneiss) into an existing set of code using the Qiime2 tutorial (https://docs.qiime2.org/2019.10/tutorials/gneiss/) to check my implementation but am struggling to replicate the qiime2 results. Does anybody knew of a tutorial or guide for doing so? I’m hoping to use the stand alone code to make it easier to share with colleagues in the future especially as I only require a small fraction of what qiime can do.

Frustratingly the main tutorial on the gneiss github page (https://github.com/biocore/gneiss/blob/master/ipynb/balance_trees.ipynb) references functions that are no longer part of the library while the subsequent tutorials seem to rely on using qiime to calculate the core results and then just use python for visualisation.

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Hi @cwduffy, yes there is an Python API available. The documentation + code snippets is found here: https://biocore.github.io/gneiss/docs/v0.4.0/index.html

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