Update README to give Rerio download instructions in the getting star…

…ted section.

README.rst

@@ -84,15 +84,33 @@ Megalodon is accessed via the command line interface ``megalodon`` command.
 
     # Example command to output basecalls, mappings, and CpG methylation in both per-read (``mod_mappings``) and aggregated (``mods``) formats
     #   Compute settings: GPU devices 0 and 1 with 40 CPU cores
-    # For highest accuracy methylation calls see research models in Rerio: https://github.com/nanoporetech/rerio
-    megalodon raw_fast5s/ \
+    megalodon \
+        raw_fast5s/ \
         --outputs basecalls mappings mod_mappings mods \
         --reference reference.fa --mod-motif Z CG 0 \
         --devices 0 1 --processes 40
 
 This command produces the ``megalodon_results`` output directory containing all requested output files and logs.
 The format for common outputs is described briefly below and in more detail in the `full documentation <https://nanoporetech.github.io/megalodon/>`_
 
+The above command uses the modified base model included in Guppy (more details below `Guppy Models and Parameters`_).
+As more accurate basecalling models are trained, they are first released into the `Rerio repository for research models <https://github.com/nanoporetech/rerio>`_.
+Once training pipelines are more thoroughly standardized and tested models will be transferred into Guppy.
+The code below shows how to obtain and run the R9.4.1, MinION/GridION, 5mC CpG model (more accurate 5mC CpG methylation results than default model).
+
+::
+
+    # Obtain and run R9.4.1, MinION, 5mC CpG model from Rerio
+    git clone https://github.com/nanoporetech/rerio
+    rerio/download_model.py rerio/basecall_models/res_dna_r941_min_modbases_5mC_CpG_v001
+    megalodon \
+        raw_fast5s/ \
+        --guppy-params "-d ./rerio/basecall_models/" \
+        --guppy-config res_dna_r941_min_modbases_5mC_CpG_v001.cfg \
+        --outputs basecalls mappings mod_mappings mods \
+        --reference reference.fa --mod-motif m CG 0 \
+        --devices 0 1 --processes 40
+
 ..
 
     The path to the ``guppy_basecall_server`` executable is required to run Megalodon.
@@ -157,7 +175,7 @@ Megalodon will continue to search for FAST5s until the ``final_summary*`` file i
 Guppy Models and Parameters
 ---------------------------
 
-The Guppy model defines the modified bases capable of being output by Megalodon.
+The basecalling model defines the modified bases capable of being output by Megalodon.
 Basecalling models must be trained to specifically detect a type or types of modified bases.
 See the `Megalodon documentation here <https://nanoporetech.github.io/megalodon/modbase_training.html>`_ for instructions to construct modified base training data and train a new modified base model.
 

docs/conf.py

@@ -26,7 +26,8 @@
 # include 'sphinx.ext.autodoc' for API documentation
 extensions = ['sphinx.ext.viewcode',
               'sphinx.ext.intersphinx', 'sphinx.ext.mathjax', 'sphinxarg.ext',
-              'sphinx.ext.napoleon',]
+              'sphinx.ext.napoleon',
+              'sphinx.ext.autosectionlabel']
 mathjax_path = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
 
 # don't include class inheritence in docs: https://stackoverflow.com/questions/46279030/how-can-i-prevent-sphinx-from-listing-object-as-a-base-class