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Blockkurs MicrobialBioinfo
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@@ -203,10 +203,13 @@ Change the variables to your needs.
### DOWNLOAD
T
RE
E FILE
S
### DOWNLOAD RE
SULT
S
The complete output for the SNP calling, MSA and tree can be found here, download it into a
`[target_directory]`
of your choice.
In every snippy folder you will find a folder called
`iqtree`
containing the phylogenetic tree (the .tre file).
```
bash
# Typestrain as reference
cp
-r
/shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/illumina/03_output_mrsa/snippy_ref_typestrain
[
target_directory]
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