Reference sequence databases: SILVA

Create a conda environment (if not created before)

conda env create -f utilities/snakemake37_environment.yml

Go to the utilities folder of silva

cd galaxy-tool-BLAST/utilities/silva

Activate the environment

conda activate snakemake37

To create the databases execute the snakefile

snakemake -j 2

The description below is made for the manual creation of the database and is deprecated but can still be useful

Create SILVA blast database with taxonomy

Download SILVA SSUParc fasta file

wget https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/SILVA_132_SSUParc_tax_silva.fasta.gz
gunzip SILVA_132_SSUParc_tax_silva.fasta.gz

Download SILVA SSUParc taxonomy file

wget https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/taxmap_slv_ssu_parc_132.txt.gz
gunzip taxmap_slv_ssu_parc_132.txt.gz

Create fasta file with taxonomy

python utilities/silva/add_taxonomy_silva.py -f SILVA_132_SSUParc_tax_silva.fasta -t taxmap_slv_ssu_parc_132.txt -o SILVA_132_SSUParc_tax_silva_taxonomy.fasta    

Make blast database

makeblastdb -in SILVA_132_SSUParc_tax_silva_taxonomy.fasta -dbtype nucl