Running Makeblastdb with large input files

voidnyx

Junior Member

Join Date: Jun 2015

Posts: 7
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#1

Running Makeblastdb with large input files

12-03-2015, 02:54 AM

Hi,

I am currently trying to make a blast'able database from a set of DNA reads. My reads-file is ~37GB in size and I was wondering if there is a way to speed up the makeblastdb step?

Is it possible to split my .fa file and run multiple instances of makeblastdb parallel without messing up my final db-file? Is there a way to use more than just one core for the program?

thanks for any ideas.
Tags: blast, large file, makeblastdb
maubp

Peter (Biopython etc)

Join Date: Jul 2009

Posts: 1544
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#2

12-03-2015, 03:28 PM

You could make several small databases, then combine them with an alias file like the NCBI do for the NR and NT databases etc.
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Running Makeblastdb with large input files

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