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Update Bioinformatics scripts authored by aneves's avatar aneves
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Bioinformatics-scripts.md
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......@@ -9,6 +9,7 @@ Performs reads trimming and computes quality control metrics.
| FastQC | FastQC-0.11.8 |
| Contamination level | Kraken-1.1 |
### Quality 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 | Green | Orange | Red | Description |
......@@ -17,3 +18,6 @@ Based on the output, 3 quality metrics and a quality score (green/orange/red) ar
| 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
# Script 01
[01-SNP_calling.sh](https://gitlab.isb-sib.ch/SPSP/spsp-tools/blob/master/pipeline/01-SNP_calling.sh)