Updating manual

README.rst

-README
-========
 
 .. image::      docs/source/_images/frangiPANe.png
 
-FrangiPANe
-=========
-
-FrangiPANe is a tool designed to simplify the construction of a pan-reference using the map-then-assembly approach.
-It was previously developed as a modular and interactive application based on Jupyter Book.
 
-It has now been recoded and integrated into a Snakemake pipeline.
+FrangiPANe
+    a tool designed to simplify the construction of a pan-reference using the map-then-assembly approach.
+Previously developed as a modular and interactive application based on Jupyter Book [1]_ , it has now been recoded and integrated into a Snakemake pipeline.
 
 
 I - Installing FrangiPANe
--------------
+-------------------
 
 **Requirement**
 
-- [Git](https://git-scm.com/)
-- [Singularity](https://...)
+- `Git <https://git-scm.com/>`_
+
+- `Singularity <https://...>`_
 
 
 **Clone the git repository**
@@ -37,11 +33,11 @@ I - Installing FrangiPANe
     python3 -m pip install -e .
 
 
-**Updating snakecdysis package (ref) using by frangiPANe if necessary**
+.. code-block:: rst
 
-::
+    NOTE : Updating snakecdysis package (ref) using by frangiPANe if necessary
 
-python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
+        python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
 
 **Install frangiPANe tool**
 
@@ -142,6 +138,7 @@ III - Run FrangiPANe
 **cluster mode**
 
 ::
+    module load python/3.8.12
 
     frangiPANe run_cluster -c /scratch/tranchant/data_test_config.RN.yaml --cluster-config /scratch/tranchant/frangipane/frangiPANe/install_files/cluster_config_ITROP.yaml
 
@@ -213,3 +210,8 @@ Licence
 -  Intellectual property belongs to IRD/UMR DIADE.
 
 -  Copyright 2024
+
+Reference
+--------------
+
+.. [1] Christine Tranchant-Dubreuil and al. (2023). FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genom Bioinform. doi: 10.1093/nargab/lqad013..