Question: Makeblastdb - parallel speed ups?
0
gravatar for jeremy.cox.2
4.2 years ago by
jeremy.cox.290
United States
jeremy.cox.290 wrote:

Hello All,

I am new to curating Blast databases.  We use a complete nucleotide database based on NCBI database.  
14 months ago, that was 26 GB and took about 26 hours on our system to compile.

Is it possible to makeblastdb using any sort of parallelism to speed it up?

Perhaps I can make separate blast db and then combine them somehow?

 

Thanks for any tips,

Jeremy Cox

blast • 1.8k views
ADD COMMENTlink modified 4.2 years ago by Siva1.6k • written 4.2 years ago by jeremy.cox.290
1
gravatar for Siva
4.2 years ago by
Siva1.6k
United States
Siva1.6k wrote:

Could you not use the pre-formatted BLAST databases from NCBI?

If you want to create your own BLAST database, you can split the sequences and create several BLAST databases.

You can either use the list of databases as an option to -db when running BLAST

-db "BLAST_DB1 BLAST_DB2"

or you can use blastdb_aliastool to create an alias for these databases.

ADD COMMENTlink written 4.2 years ago by Siva1.6k
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