.. |PipeCraft2_logo| image:: _static/PipeCraft2_icon_v2.png
  :width: 50
  :target: https://github.com/pipecraft2/pipecraft

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    <style> .red {color:#ff0000; font-weight:bold; font-size:16px} </style>

.. role:: red

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    <style> .green {color:#00f03d; font-weight:bold; font-size:16px} </style>

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.. meta::
    :description lang=en:
        PipeCraft manual. tutorial

.. _example_analyses:

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Example data analyses |PipeCraft2_logo|
=======================================

This section provides end-to-end examples for PipeCraft2 pre-compiled pipelines, showing what inputs
to use, which key settings matter and what outputs to expect.

The examples are also a good way to learn the **post-processing** logic in PipeCraft2. Different pipelines (and
marker types) may filter, curate, and summarize results in slightly different ways, so it is worth browsing
multiple examples and comparing their post-processing steps and outputs.


.. toctree::
   :maxdepth: 1

   example_analyses_QC
   example_analyses_DADA2_16S
   example_analyses_DADA2_COI
   example_analyses_DADA2_ITS
   example_analyses_vsearchOTU
   example_analyses_OptimOTU
   example_analyses_NextITS
   example_analyses_FunBarONT