Bioinformatics-scripts.md

@@ -11,9 +11,9 @@ Performs reads trimming and computes quality control metrics.
 
 Based on the output, 3 quality metrics and a quality score (green/orange/red) are computed in script [generate_trimming-cleaning_report.pl](https://gitlab.isb-sib.ch/SPSP/spsp-tools/blob/master/pipeline/generate_trimming-cleaning_report.pl). The consensus from [Bioinformatics_consensus_v1.xlsx](https://gitlab.isb-sib.ch/SPSP/spsp-tools/blob/master/Bioinformatics_consensus_v1.xlsx) is summarized in the table below:
 
-| Metric | Description | Green | Orange | Red |
+| Metric  | Green | Orange | Red | Description |
 | ------ | ------ | ------ | ------ | ------ |
-| Contamination [%]| Percent reads corresponding to another order than the expected one |  <= 0.2% | > 0.2% & <= 5% | > 5% | 
-| Read length after trimming [%] | >= 75% | >= 67% & < 75% | < 67% | 
-| Coverage [X] | >= 60X | >= 30X & < 60X | < 30X | 
+| Contamination [%] | [0,0.2] | ]0.2,5] | ]5,Inf[ | Percent reads corresponding to another order than the expected one |
+| Read length after trimming [%] |  [75,100] | [67,75[ | [0,67[ | median(read length after trimming)/median(read length before trimming) |
+| Coverage [X] | [60,100] | [30,60[ | [0,30[ | number_of_reads * median(read length after trimming)/genome_length