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Update Bioinformatics scripts
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Feb 03, 2020
by
aneves
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@@ -21,3 +21,11 @@ Based on the output, 3 quality metrics and a quality score (green/orange/red) ar
# Script 01
[01-SNP_calling.sh
](
https://gitlab.isb-sib.ch/SPSP/spsp-tools/blob/master/pipeline/01-SNP_calling.sh
)
Performs typing, assembly and SNP calling.
| Method | Tool |
| ------ | ------ |
| MLST | MentaLiST-0.2.4 |
| Assembly | SPAdes-3.13 |
| SNP calling (mapping) | samtools-1.9, Picard-2.18.20, BWA-0.7.17 |
| SNP calling (variant calling) | GATK-3.8.1.0, VCFtools-0.1.16 |
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