TBLASTN on a large DNA database (352GB)

Question

[chippy8899]

Hi,

I wonder if it possible to run command TBLASTN on a large metagenomic database(352G)? Wondering how long does it take if I m running on 4 cpus with memory available of 32G...

[Sishuo Wang]

I am not 100% sure but based on my experience it might take 10-30 mins for one sequence.

Answer 1

[Kamil]

USEARCH is "orders of magnitude faster than BLAST", so you might consider using that instead.

In a benchmark with 1,000 queries against a 15 Gb FASTA file containing 38.5 M proteins, USEARCH achieved a similar result to BLAST and finished in 9 minutes instead of 4.5 hours.