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bkille committed Jan 9, 2022
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# Running Parsnp
Parsnp can be run multiple ways, but the most common is with a set of genomes and a reference.
```
parsnp -g <reference_genbank> -d <genomes
parsnp -g <reference_genbank> -d <genomes>
```
```
parsnp -r <reference_fasta> -d <genomes
parsnp -r <reference_fasta> -d <genomes>
```
For example,
```
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