Changes

Page history
Update Bioinformatics scripts authored by aneves's avatar aneves
Show whitespace changes
Inline Side-by-side
Bioinformatics-scripts.md
View page @ e263f93d
# Script 00
Performs reads trimming and computes quality control metrics (please refer to [Bioinformatics_consensus_v1.xlsx](https://gitlab.isb-sib.ch/SPSP/spsp-tools/blob/master/Bioinformatics_consensus_v1.xlsx)).
[00-Trimm_reads-QC.sh](https://gitlab.isb-sib.ch/SPSP/spsp-tools/blob/master/pipeline/00-Trimm_reads-QC.sh)
Performs reads trimming and computes quality control metrics.
| Method | Tool |
| ------ | ------ |
| Reads trimming | Trimmomatic-0.38 |
| FastQC | FastQC-0.11.8 |
| Contamination level | Kraken-1.1 |
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 |
| ------ | ------ | ------ | ------ | ------ |
| 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 |