i have question for diamond blastp

[gyudae]

hi, Im student who studying bioinformatics.

i tried to annotate my metagenome data using diamond tools, and i want to get only one best alignment result for each CDS reads. I found the --max-target-seqs option, but i worry whether i can set this parameter to 1. Because they said in the explanation "Note that this parameter does not only affect the reporting, but also the algorithm as it is taken into account for heuristics that eliminate hits prior to full gapped extension."

Please tell me how can i get only one best alignment without affecting the algorithm. Or if i dont have to worry about the note, then please explain about that

thanks for reading my question

GyuDae Lee

[bbuchfink]

You can use --max-target-seqs 1 without worry normally, the effect on the accuracy is small. To not affect the algorithm you can add the --no-ranking option.