Reference.md

@@ -237,8 +237,17 @@ The [assembly Snakefile](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidr
   * results/02_assembly/02_remove_unaligned/`run`.ali.fastq: aligned and merged sequences fastq file
 
 
-#### 3. Demultiplexing
+### 3. Demultiplexing
 
+#### 3.1. Assign each sequence record to the corresponding `sample`
+
+[assign_sequences](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/03_demultiplex/rules/assign_sequences.smk): assign each sequence record to the corresponding `projet`/`marker`/run`/`plaque` == `sample`
+
+* inputs:
+  * results/02_assembly/02_remove_unaligned/`run`.ali.fastq: aligned and merged sequences fastq file
+  * `marker` sample description .dat file
+* output:
+  * results/03_demultiplex/01_assign_sequences/`projet`/`marker`/run`.ali.assigned.fastq
 
 
 
@@ -257,10 +266,6 @@ The [assembly Snakefile](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidr
 
 
 
-## assemble
-### Paired end alignment then keep reads with quality > 40
-### Remove unaligned sequence records
-## demultiplex
 ### Assign each sequence record to the corresponding sample/marker combination
 ### Split the input sequence file in a set of subfiles according to the values of attribute `sample`
 ## filter samples