Reference.md

@@ -303,24 +303,29 @@ The [assembly Snakefile](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidr
     * results/04_filter_samples/04_filtered/`projet`/`marker`/`run`/`sample`.c.r.l.u.fasta : cleaned sequences fasta file
 
 
-### 5 Taxonomic assignment and format
+### 5. Taxonomic assignment and format
 
-We concatenate  `projet`/`marker`/`run`/`sample` .fasta files into `projet`/`marker`/`run` .fasta files
+We concatenate  `projet`/`marker`/`run`/`sample` .fasta files into `projet`/`marker`/`run` .fasta files. Then we can run the [assignment Snakefile](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/05_assignment/Snakefile).
 
-Then we can run the Snakefile.
+#### 5.1. Dereplicate sequences at `run` level
 
 
 
+#### 5.2. Taxonomic assignment
 
-## concatenate samples into run
-## assignment
-### Dereplicate and merge samples together
-### Assign each sequence to a taxon
-### Some unuseful attributes can be removed at this stage
-### The sequences can be sorted by decreasing order of count
-### Generate a table final results
+Assign each sequence to a taxon
 
+#### 5.3. Remove not relevant attributes
 
+Some attributes can be removed at this stage
+
+#### 5.4. Sort sequences
+
+The sequences can be sorted by decreasing order of count
+
+#### 5.5. Generate species occurrence final tables
+
+Generate a table final results