Open armish opened 5 years ago
Hi @armish thanks for that and the report in our other repo.
I knew the definition wasn't straightforward but I was surprised to read that paper... do you know anyone else tackling this, and what workarounds they're using (other than setting a larger N and filtering post-BLAST)?
Cheers joe
do you know anyone else tackling this, and what workarounds they're using (other than setting a larger N and filtering post-BLAST)?
lots of people actually: relevant Twitter thread. Not sure if there is an easy generic workaround, though. I would keep an eye on the current discussions.
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: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)