Add ASaiM-MT documentation

tutorials_tours.rst

@@ -18,6 +18,10 @@ We then developed `several tutorials with hands-one about metagenomics <http://g
 
         In this tutorial the `Standard Operating Procedure (SOP) <https://www.mothur.org/wiki/MiSeq_SOP>`_ for MiSeq data, developed by the creators of the Mothur software package, is perfomed within Galaxy.
 
+    `ASaiM-MT: Metatranscriptomics analysis using microbiome RNA-seq data <https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/metatranscriptomics/tutorial.html>`_
+
+        Metatranscriptomics analysis enables understanding of how the microbiome responds to the environment by studying the functional analysis of genes expressed by the microbiome. In this tutorial, we will analyze time-series data of a microbial community inside a bioreactor
+
 These tutorials can be run on ASaiM. We used then during several workshops on metagenomics data analysis using ASaiM as training support.
 
 These tutorials are also accessible directly from ASAiM.
@@ -41,4 +45,4 @@ All the tours can be accessed inside Galaxy:
 - Click on 'Help' (top panel)
 - Click on 'Interactive Tours'
 - Choose the tours you want
-- Enjoy!
+- Enjoy!

workflows.rst

@@ -69,6 +69,27 @@ The tools used in the EBI Metagenomics pipeline are also available in ASaiM. We
 
 Analyses made in EBI Metagenomics website can be then reproduced locally, without having to wait for availability of EBI Metagenomics or to upload any data on EBI Metagenomics. However the parameters must be defined by the user as we can not find them on EBI Metagenomics documentation.
 
+ASaiM-MT: ASaiM-MT: Optimized workflow for metatranscriptomics data analysis
+----------------------------------------------------------------------------
+
+While the shotgun workflow is suitable for both metagenomics and metatranscriptomics data, we also offer a dedicated workflow optimized for metatranscriptomics datasets
+
+.. figure:: /assets/images/framework/asaim-mt_workflow.png
+    :align: center
+
+    ASaiM-MT metatranscriptomics workflow
+
+The workflow is divided into 4 parts:
+
+1. Preprocessing - Process raw metatranscriptomics data to perform further analysis.
+2. Taxonomy Quantitation - Assignment of taxonomy along with abundance values and visualization.
+3. Functional Quantitation - metabolic assignment of identified functions and gene and pathway abundance annotation.
+4. Taxonomy-Function Quantitation - combine taxonomy and functional quantitation values into relative abundance values at different levels such as e.g. the abundance of a pathway between phyla.
+
+
+
+
+
 .. rubric:: References
 
 .. bibliography:: /assets/references.bib