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bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
GNU General Public License v3.0
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Assembling reads before diamond #565

Open eousley opened 2 years ago

eousley commented 2 years ago

Hi, I am currently trying to use diamond on my 250bp paired end reads separately to the use the daa2rma tool from MEGAN to combine the output files and run MEGAN. I am working with 128 cores on 512 GBs. I have also tried to -b5 -c1 -k1 to speed up Diamond, however it is still taking over 6 hours to run. I was wondering if assembling my paired end reads together using something like Megahit will help Diamond run more efficiently?

My current code: $diamond blastx -d nrd.dmnd -q Read.R1.fastq -o Read.R1.daa -b5 -c1 -k1

I am using the NCBI database.

Thanks, Emalee

bbuchfink commented 2 years ago

Yes assembly will usually reduce the amount of data by a pretty big factor.

eousley commented 2 years ago

Thank you for you response! It still took about 4 hours but it worked!