Unity
  1. Unity
  2. Documentation
  3. Datasets
  4. Bioinformatics
  5. NCBI BLAST databases

NCBI BLAST databases

The NCBI databases are downloaded every Sunday to a directory with that date. The file /datasets/bio/ncbi-db/.ncbirc is then updated to point to the new copy once the download has been verified. This allows running jobs to have a consistent database throughout the run.

Note that other tools that can use the NCBI database but do not read this configuration file can use the output of blastdb_path to find the current copy, as shown in the following example:

module load blast-plus/2.13.0+py3.8.12 diamond/2.0.15+py2.7.18
NR=$(blastdb_path -db nr -dbtype prot)
diamond blastp --db "$NR" -q query.fasta -o matches.tsv
Path:/datasets/bio/ncbi-db/
URL:https://ftp.ncbi.nlm.nih.gov/blast/db/
Downloaded:weekly
Cite:https://support.nlm.nih.gov/knowledgebase/article/KA-03391/en-us
Last modified: Sunday, July 21, 2024 at 10:09 PM. See the commit on GitLab.
University of Massachusetts Amherst University of Rhode Island University of Massachusetts Dartmouth University of Massachusetts Lowell University of Massachusetts Boston Mount Holyoke College