--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/topics/metagenomics/tutorials/dada2/tutorial.md	Mon Feb 01 20:22:27 2021 +0000
@@ -0,0 +1,642 @@
+---
+layout: tutorial_hands_on
+
+title: 16S Microbial Analysis with mothur (extended)
+zenodo_link: https://doi.org/10.5281/zenodo.800651
+questions:
+- What is the effect of normal variation in the gut microbiome on host health?
+objectives:
+- Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy
+- Using a mock community to assess the error rate of your sequencing experiment
+- Visualize sample diversity using Krona and Phinch
+time_estimation: ''
+key_points:
+- 16S rRNA gene sequencing analysis results depend on the many algorithms used and
+  their settings
+- Quality control and cleaning of your data is a crucial step in order to obtain optimal
+  results
+- Adding a mock community to serve as a control sample can help you asses the error
+  rate of your experimental setup
+- We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations
+contributors:
+- shiltemann
+- bebatut
+- tnabtaf
+
+---
+
+
+# Introduction
+{:.no_toc}
+
+<!-- This is a comment. -->
+
+General introduction about the topic and then an introduction of the
+tutorial (the questions and the objectives). It is nice also to have a
+scheme to sum up the pipeline used during the tutorial. The idea is to
+give to trainees insight into the content of the tutorial and the (theoretical
+and technical) key concepts they will learn.
+
+You may want to cite some publications; this can be done by adding citations to the
+bibliography file (`tutorial.bib` file next to your `tutorial.md` file). These citations
+must be in bibtex format. If you have the DOI for the paper you wish to cite, you can
+get the corresponding bibtex entry using [doi2bib.org](https://doi2bib.org).
+
+With the example you will find in the `tutorial.bib` file, you can add a citation to
+this article here in your tutorial like this:
+{% raw %} `{% cite Batut2018 %}`{% endraw %}.
+This will be rendered like this: {% cite Batut2018 %}, and links to a
+[bibliography section](#bibliography) which will automatically be created at the end of the
+tutorial.
+
+
+**Please follow our
+[tutorial to learn how to fill the Markdown]({{ site.baseurl }}/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html)**
+
+> ### Agenda
+>
+> In this tutorial, we will cover:
+>
+> 1. TOC
+> {:toc}
+>
+{: .agenda}
+
+# Title for your first section
+
+Give some background about what the trainees will be doing in the section.
+Remember that many people reading your materials will likely be novices,
+so make sure to explain all the relevant concepts.
+
+## Title for a subsection
+Section and subsection titles will be displayed in the tutorial index on the left side of
+the page, so try to make them informative and concise!
+
+# Hands-on Sections
+Below are a series of hand-on boxes, one for each tool in your workflow file.
+Often you may wish to combine several boxes into one or make other adjustments such
+as breaking the tutorial into sections, we encourage you to make such changes as you
+see fit, this is just a starting point :)
+
+Anywhere you find the word "***TODO***", there is something that needs to be changed
+depending on the specifics of your tutorial.
+
+have fun!
+
+## Get data
+
+> ### {% icon hands_on %} Hands-on: Data upload
+>
+> 1. Create a new history for this tutorial
+> 2. Import the files from [Zenodo]() or from the shared data library
+>
+>    ```
+>    
+>    ```
+>    ***TODO***: *Add the files by the ones on Zenodo here (if not added)*
+>
+>    ***TODO***: *Remove the useless files (if added)*
+>
+>    {% include snippets/import_via_link.md %}
+>    {% include snippets/import_from_data_library.md %}
+>
+> 3. Rename the datasets
+> 4. Check that the datatype
+>
+>    {% include snippets/change_datatype.md datatype="datatypes" %}
+>
+> 5. Add to each database a tag corresponding to ...
+>
+>    {% include snippets/add_tag.md %}
+>
+{: .hands_on}
+
+# Title of the section usually corresponding to a big step in the analysis
+
+It comes first a description of the step: some background and some theory.
+Some image can be added there to support the theory explanation:
+
+![Alternative text](../../images/image_name "Legend of the image")
+
+The idea is to keep the theory description before quite simple to focus more on the practical part.
+
+***TODO***: *Consider adding a detail box to expand the theory*
+
+> ### {% icon details %} More details about the theory
+>
+> But to describe more details, it is possible to use the detail boxes which are expandable
+>
+{: .details}
+
+A big step can have several subsections or sub steps:
+
+
+## Sub-step with **dada2_plotComplexity**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_plotComplexity** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_plotQualityProfile**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_filterAndTrim**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_filterAndTrim** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_plotComplexity**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_plotComplexity** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_plotQualityProfile**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_plotQualityProfile** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **Unzip Collection**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **Unzip Collection** {% icon tool %} with the following parameters:
+>    - {% icon param-file %} *"Input Paired Dataset"*: `paired_output` (output of **dada2_filterAndTrim** {% icon tool %})
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_learnErrors**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_learnErrors** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_learnErrors**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_learnErrors** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_dada**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_dada** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_dada**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_dada** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_mergePairs**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_mergePairs** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_makeSequenceTable**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_makeSequenceTable** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_removeBimeraDenovo**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_removeBimeraDenovo** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_seqCounts**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_seqCounts** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+## Sub-step with **dada2_assignTaxonomyAddspecies**
+
+> ### {% icon hands_on %} Hands-on: Task description
+>
+> 1. **dada2_assignTaxonomyAddspecies** {% icon tool %} with the following parameters:
+>
+>    ***TODO***: *Check parameter descriptions*
+>
+>    ***TODO***: *Consider adding a comment or tip box*
+>
+>    > ### {% icon comment %} Comment
+>    >
+>    > A comment about the tool or something else. This box can also be in the main text
+>    {: .comment}
+>
+{: .hands_on}
+
+***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
+
+> ### {% icon question %} Questions
+>
+> 1. Question1?
+> 2. Question2?
+>
+> > ### {% icon solution %} Solution
+> >
+> > 1. Answer for question1
+> > 2. Answer for question2
+> >
+> {: .solution}
+>
+{: .question}
+
+
+## Re-arrange
+
+To create the template, each step of the workflow had its own subsection.
+
+***TODO***: *Re-arrange the generated subsections into sections or other subsections.
+Consider merging some hands-on boxes to have a meaningful flow of the analyses*
+
+# Conclusion
+{:.no_toc}
+
+Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the
+pipeline used.
\ No newline at end of file