.. _index_tutorials:

===================
QIIME Tutorials
===================
The QIIME tutorials are documents that illustrate how to use various features of the QIIME. We recommend that all users begin with the `QIIME overview tutorial <./tutorial.html>`_ which takes the user through a full analysis of sequencing data. After you've begun analyzing your own data, you'll want to move on to the special-purpose tutorials as needed. 

The QIIME development team is very interested in incorporating community-contributed tutorials. Please contact the `QIIME Forum <http://groups.google.com/group/qiime-forum>`_ if you're interested in contributing.


**Getting started: Sequence processing through OTU tables and phylogenetic trees**

.. toctree::
   :maxdepth: 1

   otu_picking
   illumina_overview_tutorial
   tutorial
   open_reference_illumina_processing
   fungal_its_analysis
   processing_illumina_data
   processing_18S_data
   working_with_biom_tables

**Additional Quality Control**

.. toctree::
   :maxdepth: 1

   denoising_454_data
   chimera_checking
   usearch_quality_filter
   denoising_and_chimera_detection_usage_comparison

**Alternative Processing Steps**

.. toctree::
   :maxdepth: 1

   rtax
   retraining_rdp
   predicting_mislabeled_samples
   filtering_contamination_otus
   chaining_otu_pickers

**Analyzing diversity**

.. toctree::
   :maxdepth: 1

   category_comparison
   creating_distance_comparison_plots
   distance_matrix_comparison
   taxa_summary_comparison
   making_cytoscape_networks
   running_supervised_learning
   procrustes_analysis
   source_tracking
   

**Experimental QIIME features: these tutorials cover features that should be considered beta QIIME software**

.. toctree::
   :maxdepth: 1

   shotgun_analysis

**Other**

.. toctree::
   :maxdepth: 1

   unix_commands
   working_with_aws
   parallel_qiime
   remote_mapping_files
   metadata_description
   


