kraken2-build download searches for the fasta file of the particular db one wants to download. From April'24, NCBI only provides the fasta file for a few dbs, (Nt & nr)
"In April 2024, the BLAST FASTA files in this directory will no longer be
available. You can easily generate FASTA files yourself from the formatted
BLAST databases by using the BLAST utility blastdbcmd that comes with the
standalone BLAST programs. See NCBI Insights for more details
https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/"
On the other hand, there are more precomplied databases available ( I am particularly interested in the eukaryota LSU and SSU). Would it be possible to build a kraken2 db from one of the files available from https://ftp.ncbi.nlm.nih.gov/blast/db/ ?
Hi there,
kraken2-build download searches for the fasta file of the particular db one wants to download. From April'24, NCBI only provides the fasta file for a few dbs, (Nt & nr)
"In April 2024, the BLAST FASTA files in this directory will no longer be available. You can easily generate FASTA files yourself from the formatted BLAST databases by using the BLAST utility blastdbcmd that comes with the standalone BLAST programs. See NCBI Insights for more details https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/"
On the other hand, there are more precomplied databases available ( I am particularly interested in the eukaryota LSU and SSU). Would it be possible to build a kraken2 db from one of the files available from https://ftp.ncbi.nlm.nih.gov/blast/db/ ?