Reference.md

@@ -247,40 +247,46 @@ 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
   * [sample description .dat files](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/tree/master/resources/test/sample_description): a table with 6 columns (plaque, plaque1, barcode, primer5, primer3, infos) and rows as a `plaque` element description. Each sample description file belong to a `marker` wildcard.
 * output:
-  * results/03_demultiplex/01_assign_sequences/`projet`/`marker`/`run`.ali.assigned.fastq
+  * results/03_demultiplex/01_assign_sequences/`projet`/`marker`/`run`.ali.assigned.fastq: aligned and merged sequences with assigned `sample` fastq file
 
 ###  3.2 Split `run` file into `run`/`sample` files
 
 [split_sequences](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/03_demultiplex/rules/split_sequences.smk): split the input sequence file in a set of subfiles according to the values of attribute `sample`
 
 * input:
-  * results/03_demultiplex/01_assign_sequences/`projet`/`marker`/`run`.ali.assigned.fastq
+  * results/03_demultiplex/01_assign_sequences/`projet`/`marker`/`run`.ali.assigned.fastq: sequences with assigned `sample` fastq file
 * output:
-  * results/03_demultiplex/02_raw/`projet`/`marker`/`run`/`sample`.fasta
+  * results/03_demultiplex/02_raw/`projet`/`marker`/`run`/`sample`.fasta: sequences which belong to a `sample` fasta file
 
 
 ### 4 Filtering
 
-### 5 Taxonomic assignment and format
+#### 4.1 Dereplicate sequences at `sample` level
+
+ dereplicate reads into uniq sequences
+
+
+#### 4.2 Remove sequences with wrong length or IUAPC ambiguity or low depth coverage
+
+ only sequence more than 20bp with no ambiguity IUAPC with total coverage greater than 10 reads
 
+#### 4.3 Detect PCR/sequencing errors sequences
 
+Clean the sequences for PCR/sequencing errors (sequence variants)
 
+#### 4.4 Remove PCR/sequencing errors sequences
 
-## write demultiplex table
+Remove sequence which are classified as 'internal' by obiclean
 
 
 
-## 
+
+
+### 5 Taxonomic assignment and format
+
 
 
 
-### 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
-### dereplicate reads into uniq sequences
-### only sequence more than 20bp with no ambiguity IUAPC with total coverage greater than 10 reads
-### Clean the sequences for PCR/sequencing errors (sequence variants)
-### Remove sequence which are classified as 'internal' by obiclean
 ## concatenate samples into run
 ## assignment
 ### Dereplicate and merge samples together