Merge branch 'master' of https://github.com/biocore/qiita

qiita-spots · Jul 14, 2018 · 405cbef · 405cbef
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diff --git a/qiita_pet/support_files/doc/source/europeanbioinformaticsinstitute.rst b/qiita_pet/support_files/doc/source/europeanbioinformaticsinstitute.rst
@@ -1,8 +1,14 @@
 .. role:: red
 
-EBI submission via Qiita
+EBI Submission via Qiita
 ========================
 
+  1.  Upload sample information and preparation information with their required fields for amplicon sequencing
+  2.  Link appropriate sequence files
+  3.  Run split libraries, trimming, then deblur or closed reference commands
+
+*  Note: when using closed reference make sure you're using Greengenes for 16S  :ref:`[7]<reference7>`, Silva for 18S  :ref:`[8]<reference8>`  , and UNITE for ITS  :ref:`[9]<reference9>`
+
 Qiita allows users to deposit their study, sample, experiment and sequence data to the
 `European Nucleotide Archive (ENA) <https://www.ebi.ac.uk/ena>`__, which is the permanent data
 repository of the `European Bioinformatics Institute (EBI) <https://www.ebi.ac.uk/>`__. Submitting to

diff --git a/qiita_pet/support_files/doc/source/gettingstartedguide/home_screen.png b/qiita_pet/support_files/doc/source/gettingstartedguide/home_screen.png
diff --git a/qiita_pet/support_files/doc/source/gettingstartedguide/index.rst b/qiita_pet/support_files/doc/source/gettingstartedguide/index.rst
@@ -79,11 +79,13 @@ Editing a Study
 Creating and Working With Sample information
 --------------------------------------------
 
+*  The :doc:`../qiimp` tab located at the top of the page is a useful tool for creating Qiita and EBI compatible metadata spreadsheets.
+
 Example files
 ~~~~~~~~~~~~~
 
 You can download an example sample information file from
-`here <ftp://ftp.microbio.me/pub/qiita/sample_prep_information_files_examples.tgz>`__
+`here <ftp://ftp.microbio.me/pub/qiita/sample_prep_information_files_examples.tgz>`__.
 
 EBI-ENA NULL values vocabulary
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/qiita_pet/support_files/doc/source/index.rst b/qiita_pet/support_files/doc/source/index.rst
@@ -27,6 +27,7 @@ Looking for information about getting started? Please see the document here:
    :maxdepth: 2
 
    gettingstartedguide/index.rst
+   qiimp.rst
 
 Looking for information about how to process your data? Please see the document here:
 

diff --git a/qiita_pet/support_files/doc/source/qiimp.rst b/qiita_pet/support_files/doc/source/qiimp.rst
@@ -0,0 +1,10 @@
+.. _Qiimp:
+
+.. index:: Qiimp
+
+Qiimp
+=======
+*  Helps you create Qiita and EBI compatible metadata spreadsheets
+
+For more information and  advanced queries go to the `Qiimp github page <https://github.com/ucsd-ccbb/qiimp>`__.
+For a step by step guide on using Qiimp, visit the `Qiimp tutorial <https://github.com/ucsd-ccbb/qiimp/blob/master/docs/index.r>`__.
diff --git a/qiita_pet/support_files/doc/source/tutorials/downloading.rst b/qiita_pet/support_files/doc/source/tutorials/downloading.rst
@@ -53,3 +53,11 @@ Finding Samples Based On Their Metadata
 For help on doing complex searches for samples go to :doc:`../redbiom`. Redbiom
 helps users find samples based on their metadata, a specific taxon or feature
 of interest via a simple Qiita GUI or the command line (more powerful).
+
+Moving Your Analysis From Qiita to QIIME2
+-----------------------------------------
+
+After downloading your Qiita data, you can continue your analysis in QIIME2.
+For information on transfering your data, visit the
+`Transferring Qiita Artifacts to QIIME2 <https://forum.qiime2.org/t/transferring-qiita-artifacts-to-qiime2/4790>`__
+QIIME2 community tutorial page.
diff --git a/qiita_pet/support_files/doc/source/tutorials/prepare-templates.rst b/qiita_pet/support_files/doc/source/tutorials/prepare-templates.rst
@@ -1,8 +1,8 @@
 :orphan:
 
-#.. _prepare-templates:
+.. _prepare-templates:
 
-#.. index:: prepare-templates
+.. index:: prepare-templates
 
 Templates
 =========