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:

• S19_genome_mining_and_gene_identification/scripts/Gene_mining.slurm
• S23_S25_MHC_I_target_sequence_generation_and_read_count/scripts/MHC_U-lineage_consensus.sh
• S23_S25_MHC_I_target_sequence_generation_and_read_count/scripts/MHC_Z-lineage_consensus.sh

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)

[mmatschiner]

Hi Arman,

thanks for pointing to this. We certainly were not aware of the issues that were raised regarding max_target_seqs when we wrote the script. But based on reports following to the publication of Shah et al., such as https://blastedbio.blogspot.com/2018/11/blast-max-alignment-limits-repartee-two.html we do not expect that this option affected our results.

Best regards, Michael