mashID database it identify mycobacteria

db_fodler=/media/36tb/db/mashID/mycoID<br># Mbovis mashID db updatehttps://github.com/duceppemo/mashID<br># Download RefSeq -&gt; 10719conda activate ncbibash ~/prog/ncbi/refseqDownloader.sh \ -d bacteria \ -q "Mycobacterium,Mycolicibacterium,Mycolicibacter,Mycolicibacillus,Mycobacteroides" \ -u \ -f fna \ -o "$db_fodler" \ -r<br>conda deactivate<br># Remove bad downloads -&gt; 19rm "${db_fodler}"/*.gz<br># Remove Mycobacterium sp. -&gt; 290find "$db_fodler" -name "*_sp_*" -exec rm {} \;<br># Derepconda activate mashIDpython ~/prog/Assembly-Dereplicator/dereplicator.py \ --distance 0.001 \ --threads $(nproc) \ "${db_fodler}"/fna \ "${db_fodler}"/fna_derep_0.001<br>conda deactivate<br><br># Add bovis ref genomeconda activate ncbibash get_assemblies_v2.sh \ -q NC_002945.4 \ -t refseq \ -o "${db_fodler}"/fna_derep_0.001 \ -r \ -u<br>conda deactivate<br>conda activate mashIDpython ~/prog/mashID/make_mashID_db.py \ -i "${db_fodler}"/fna_derep_0.001 \ -o /media/36tb/db/mashID \ -p mycobacteria_2024-02-23.msh \ -t $(nproc) \ -s 10000 \ -k 21<br><br>baseDir=/home/bioinfo/analyses/MBWGS051<br>python ~/prog/mashID/mashID.py \ -i "${baseDir}"/fastq \ -o "${baseDir}"mashID \ -d /media/36tb/db/mashID/mycobacteria_2024-02-23.msh \ -p 3 <br><br>