Create Local BLAST Database

The basic way to create a local BLAST database is to use the makeblastdb command:

$ makeblastdb -in input_reads.fasta -dbtype [nucl|prot] -out input_reads_db

where input_reads.fasta is the input file containing all sequences that need to be made into a database, and dbtype can be either nucl or prot depending on the type of the input file.

Simple example of how makeblastdb can be run on Swan using SLURM script and nucleotide database is shown below:

blast_db.submit

#!/bin/bash
#SBATCH --job-name=Blast_DB
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=168:00:00
#SBATCH --mem=10gb
#SBATCH --output=BlastDB.%J.out
#SBATCH --error=BlastDB.%J.err

module load blast/2.10

makeblastdb -in input_reads.fasta -dbtype nucl -out input_reads_db

More parameters used with makeblastdb can be seen by typing:

$ makeblastdb -help