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q2-fragment-insertion replaces mafft through fastree in moving pics tutorial #293

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gregcaporaso opened this issue Mar 16, 2018 · 1 comment

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@gregcaporaso
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gregcaporaso commented Mar 16, 2018

Improvement Description
Here's our plan. The q2-fragment-insertion conda package is pretty large right now (182 MB as downloaded from conda), so it probably makes sense to not include this in the core distribution as it may start to overwhelm travis. So, we should hold off on putting this in the Moving Pictures tutorial until we have a plugin registry so it doesn't need to be installed for all plugin testing, etc. In the meantime, we'll add a note box to the Moving Pics tutorial with some of this info:

  • we know there are issues with the de novo tree building step - in practice, you probably want to use a reference based approach (e.g. q2-fragment-insertion) when a reference tree is available
  • there are multiple ways to go from FeatureData[Sequence] to Phylogeny[Rooted], which is the goal of these steps. this will be increasingly common as more plugins become available.
  • there are plugins outside of the core distribution that are likely to be useful to users, e.g., this one

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Discussed with @wasade at the 2018 May dev workshop.

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https://github.com/biocore/q2-fragment-insertion

@gregcaporaso gregcaporaso changed the title add note about q2-fragment-insertion to moving pics tutorial q2-fragment-insertion replaces mafft through fastree in moving pics tutorial May 11, 2018
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When making this change, we should also point out the concern brought up by @lozuponelab on the forum. If this text is getting long in the Moving Pictures tutorial, it might be worth a separate tutorial that discusses tree building, and moving the taxonomy assignment step before the phylogeny reconstruction step in Moving Pics, so users can filter poorly assigned sequences before building a tree.

@gregcaporaso gregcaporaso self-assigned this May 24, 2018
@gregcaporaso gregcaporaso removed their assignment Sep 11, 2018
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