kraken2 db from NCBI db

Format_NCBI_4_Kraken2.sh

# First download to your computer the right database from NCBI. You can either go to https://ftp.ncbi.nlm.nih.gov/blast/db/
# and download the right db, or if it is a multi-file one run
# perl <path/to/ncbi/bin>/update_blastdb.pl --decompress <name_of_db>
# I would recommend having one db per folder, as it might rewrite the taxdb.btd/bti files

######
#
## Once you have the downloaded db, the next thing is to extract the FASTA from the dbs 
# I am sure once there is a downloaded db, there is an easy way of generating the krakendb, but here we are

## USAGE: bash Format_NCBI_4_Kraken2.sh <folder_with_NCBI_db>/<NCBI_db_name> <KRAKEN_DB_NAME>
DBNAME=$2
input=$1
input_folder=$(dirname $input)
input_db=$(basename $input)

## STEP1 Extract required info from database

blastdbcmd -db $input -entry all -out "${input_folder}"/"${input_db}".txt -outfmt ">%a|kraken:taxid|%T,%s"

## STEP2 reformat as FASTA

awk -F',' '{print $1"\n"$2}' "${input_folder}"/"${input_db}".txt > "${input_folder}"/"${input_db}".fasta

## STEP3 download a taxonomy and start your custom db

kraken2-build --download-taxonomy --use-ftp --db $DBNAME

## STEP4 add the new seqs to the db

kraken2-build --add-to-library "${input_folder}"/"${input_db}".fasta --db $DBNAME