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Merged Fanny Wegner requested to merge master-patch-c5d4 into master
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```
# GENERATE A CORE SNP ALIGNMENT
snippy-core --prefix core [outdir] [outdir2] [outdir3]
snippy-core --prefix core [outdir] [outdir2] [outdir3] --ref [reference]
```
This command will give you various output, but among them is `core.aln` and `core.full.aln`. Both are fasta multiple sequence alignment, the first contains only the core SNPs, the other contains the full alignment of your reference and the samples inlcuding any invariant sites.
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