Guide for AA-only workflows#270
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Left a smattering of comments, but I can also push up additional changes to the doc if that's preferred.
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Added some small syntax and styling comments for the latest changes.
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Thanks for the guide, @jameshadfield! I liked that I could start from full example commands from this guide for my own analysis. This could be a tutorial eventually, if we wanted to include full commands for each standard step in a workflow along with example starting data.
Augur PR <nextstrain/augur#1958> Auspice PR <nextstrain/auspice#2040>
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