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lonelyjoeparker / oddjects-sandbox

Sandbox for odd projects, mainly R / Python and mainly bioinformatics or spatial/policy social data
GNU General Public License v3.0
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Confirm that use of BLAST's `-max_target_seqs` is intentional #1

Open armish opened 5 years ago

armish commented 5 years ago

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)

lonelyjoeparker commented 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

armish commented 5 years ago

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.