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 Trying to deconvolve single tag assignment for multiple molecules
 
-## Run the deconvolution
+## Scripts
 
-    python3 src/deconvolve.py
+For the majority of the scripts, argparse is used.
+To know how to use it please use the -h option.
+
+### Data simulation
+
+* generate_fake_molecule_graph.py: Create a linear molecule graph, where the molecules are linked to the d molecules on their left and d molecules on their right.
+
+* generate_fake_barcode_graph.py: Take a barcode graph as input (gexf formated) and outputs a barcode graph. The barcode graph is create by fusion of nodes from the molecule graph.
+
+### Data structures and algorithms
+
+* to_d2_graph.py: Mount a barcode graph into memory and create a d2 graph from it.
+
+* evaluate.py: take a d2 graph gexf file and and analyse it. Look for an approximation of the longest correct path to reconstruct a molecule graph. Take as input a d2 graph where the truth is known in the node names (the format used to create fake data).
+
+* analyse_d2_tsv.py: Take an tsv optimization file of a d2 graph and look for the variables coverage. Outputs the missing variables (if exists).
 
 ## Run the tests