makeblastdb performance benchmark
Hello everyone!
Recently I've had to allocate some resources to build a blast database, but then I realized I had no idea of how many I had to give.
Doing some research around I didn't find anything answering my question: has anyone ever done some benchmarking on runtime and memory consumption for makeblastdb? For example, given n input sequences, what is the complexity of the complete set of computations made by makeblastdb?
• 1,425 views
•
link
written
by
drquestion •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Canu Nanopore Genome assembly optimization
written by SomeOne •
-
Cytoscape plugin CoExpNetViz giving unreproducible results over time
written by Raito92
-
Whole Exome Sequencing analysis pipeline
written by Rick P •
-
Tutorial: Best of Python
written by nows1997 •
-
Forum: transfer from computations to experiments?
written by dl_fgt •
-
Forum: How long does it take to build a pipeline?
written by lamteva.vera
-
memory consumption of bwa-mem
written by Lars
-
Canu assembler : meryl failed after 2 attempts
written by Rox
-
Problems with BLAST db, maybe install issue?
written by sstevens2 •
-
Publishing improved versions of algorithms - ethics and norms.
written by Endre Bakken Stovner
Someone may have a more analytical answer, but in my experience this is something you need not worry about. For a large database - no quite nr but maybe 3-4x smaller - the index database will be created in a matter of minutes. So it may be closer to an hour for nr, but I don't think you need to prepare for it other than having a good amount of memory and disk space.
Thank you very much, it took around one hour and a half for the whole UniProt sequences database, indeed!