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For consistency with other files in this project.
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victorlin committed Apr 25, 2024
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10 changes: 5 additions & 5 deletions src/guides/bioinformatics/filtering-and-subsampling.rst
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Expand Up @@ -9,7 +9,7 @@ sample data.
:local:

Filtering
---------
=========

The filter command allows you to select various subsets of your input data for
different types of analysis. A simple example use of this command would be
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--output-metadata filtered_metadata.tsv
Subsampling within ``augur filter``
-----------------------------------
===================================

Another common filtering operation is subsetting of data to a achieve a more
even spatio-temporal distribution or to cut-down data set size to more
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--output-metadata subsampled_metadata.tsv
Subsampling using multiple ``augur filter`` commands
----------------------------------------------------
====================================================

There are some subsampling strategies in which a single call to ``augur filter``
does not suffice. One such strategy is "tiered subsampling". In this strategy,
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3. Combine the samples.

Calling ``augur filter`` multiple times
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
---------------------------------------

A basic approach is to run the ``augur filter`` commands directly. This works
well for ad-hoc analyses.
Expand Down Expand Up @@ -130,7 +130,7 @@ files. If the same strain appears in both files, ``augur filter`` will only
write it once in each of the final outputs.

Generalizing subsampling in a workflow
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
--------------------------------------

The approach above can be cumbersome with more intermediate samples. To
generalize this process and allow for more flexibility, a workflow management
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