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updated formatting for docs/usage.md under kraken2 build section
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kyleoconnell committed Jan 3, 2024
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Expand Up @@ -147,23 +147,23 @@ Install mamba
bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge
```
Add mamba to your PATH
`export PATH=$PATH:/your/mamba/directory/path/bin`
```export PATH=$PATH:/your/mamba/directory/path/bin
```
Install Kraken2
`mamba install -c bioconda kraken2 -y`
```mamba install -c bioconda kraken2 -y
```
Copy all your fasta files to a directory, in this case, Fasta_dir
Now add the add to library command to add your fasta files to the kraken database
Now use the `add to library`` command to add your fasta files to the kraken database
```
for fasta in Fasta_dir/* ;
do kraken2-build --add-to-library $fasta --db orthopox_kdb --threads $THREADS;
done
```
Download the reference NCBI taxonomy files
```
kraken2-build --download-taxonomy --db orthopox_kdb --threads $THREADS
```kraken2-build --download-taxonomy --db orthopox_kdb --threads $THREADS
```
Now build the database
```
kraken2-build --build --db orthopox_kdb --threads $THREADS
```kraken2-build --build --db orthopox_kdb --threads $THREADS
```

## Running the pipeline
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