making_reference_database

#######making reference database########

#information on Centrifuge tool can be found here https://ccb.jhu.edu/software/centrifuge/ and https://github.com/DaehwanKimLab/centrifuge

module load blast/2.10
module load anaconda
conda activate centrifuge

#download all archaea, bacteria and viruses from NCBI
centrifuge-download -o library -m -d "archaea,bacteria,viral" refseq > seqid2taxid.map

#to download swine and cattle genomes from NCBI
centrifuge-download -o library -d "vertebrate_mammalian" -a "Chromosome" -t 9823 refseq >> seqid2taxid.map
centrifuge-download -o library -d "vertebrate_mammalian" -a "Chromosome" -t 9913 refseq >> seqid2taxid.map

#building the reference database
centrifuge-build -p 16 --conversion-table seqid2taxid_all.map --taxonomy-tree taxonomy/nodes.dmp --name-table taxonomy/names.dmp all_new.fna new_all