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Download files from the Silva website We need the following files: SILVA_xxx_SSURef_NR99_tax_silva.fasta. SILVA_xxx_LSURef_tax_silva.fasta.
gtdb_migration_tk --ssu_ref SILVA_xxx_SSURef_NR99_tax_silva.fasta --lsu_ref SILVA_xxx_LSURef_tax_silva.fasta -o /srv/db/silva/<silva_version>/ -l /path/to/log/directory
gtdb_migration_tk --ssu_ref SILVA_xxx_SSURef_NR99_tax_silva.fasta --lsu_ref SILVA_xxx_LSURef_tax_silva.fasta
-o /srv/db/silva/<silva_version>/ -l /path/to/log/directory
Next step is to generate the Blast database: makeblastdb -in <fasta_file> –dbtype nucl for both files
makeblastdb -in <fasta_file> –dbtype nucl