Mash Sketch of RefSeq Bacterial Representative Genomes v217

<p>This was created to get a new mash reference that was current. The script to create this uses ncbi datasets and mash (https://github.com/UPHL-BioNGS/Grandeur/blob/main/bin/new_mash_ref.sh)<br> <br> This was created on April 27, 2023, and is RefSeq v217<br> <br> ```bash</p> <p>#/bin/bash<br> out=mash_db<br> <br> mkdir $out</p> <p>cd $out</p> <p>datasets summary genome taxon bacteria --reference --as-json-lines | \</p> <p>dataformat tsv genome --fields accession,assminfo-refseq-category,organism-name --elide-header | \</p> <p>grep representative | \</p> <p>tee representative_genomes.txt | \</p> <p>cut -f 1 &gt; genome_ids.txt</p> <p>echo &quot;$(date): Downloading genomes for ids&quot;</p> <p>datasets download genome accession --inputfile genome_ids.txt --filename rep-genomes.zip</p> <p>echo &quot;$(date): Decompressing zip file&quot;</p> <p>unzip rep-genomes.zip</p> <p>echo &quot;$(date): Creating file for mash&quot;</p> <p>cat ncbi_dataset/data/*/*.fna | sed &#39;s/ /_/g&#39; | sed &#39;s/,//g&#39; &gt; rep-genomes.fasta</p> <p>echo &quot;$(date): Skeching rep-genomes.fasta&quot;</p> <p>mash sketch -i -p 20 rep-genomes.fasta -o rep-genomes</p> <p>############################################################</p> <p>echo &quot;$(date): File preparation is complete&quot;</p> <p>ls -alh rep-genomes.fasta</p> <p>ls -alh rep-genomes.msh<br> <br> ```</p>