Mash Sketch of RefSeq Bacterial Representative Genomes v221

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)This was created on January 14, 2024, and is RefSeq v221```bash #/bin/bashout=mash_dbmkdir $out cd $out datasets summary genome taxon bacteria --reference --as-json-lines | \ dataformat tsv genome --fields accession,assminfo-refseq-category,organism-name --elide-header | \ grep representative | \ tee representative_genomes.txt | \ cut -f 1 > genome_ids.txt echo "$(date): Downloading genomes for ids" datasets download genome accession --inputfile genome_ids.txt --filename rep-genomes.zip echo "$(date): Decompressing zip file" unzip rep-genomes.zip echo "$(date): Creating file for mash" cat ncbi_dataset/data/*/*.fna | sed 's/ /_/g' | sed 's/,//g' > rep-genomes.fasta echo "$(date): Skeching rep-genomes.fasta" mash sketch -i -p 20 rep-genomes.fasta -o rep-genomes ############################################################ echo "$(date): File preparation is complete" ls -alh rep-genomes.fasta ls -alh rep-genomes.msh```