Confirm that use of BLAST's -max_target_seqs is intentional

[armish]

Hi there,

This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's -max_target_seqs parameter:

• nanopore/blastn.qsub

Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, there is a strong chance that this parameter is misused in your repository.

If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.

Thank you!
-- Arman (armish/blast-patrol)

[dfornika]

Thanks for raising this issue. I do need to take a closer look at how I'm using that parameter. I had been assuming that setting it to -max_target_seqs 1 would return the one 'best hit'. After reading the paper you linked to I realize that isn't the case, so I will need to adjust my script to account for this issue.