Does rmdup remove by identical sequences or substring patterns?

[sophiachen1]

Hi,
I have a protein fasta file and used rmdup to remove duplicated sequence (I expect to remove completely identical sequences) in the file. However, I find in my output file, it also removed a few short sequences that are substrings of another sequence. I am wondering if rmdup removes by substring pattern?

Thanks,
Sophia

[shenwei356]

add --by-seq, see also the full usage: https://bioinf.shenwei.me/seqkit/usage/#rmdup

[sophiachen1]

Hi Wei,
Thanks for your quick response. I have added -s option in my command and observed the short sequence removal and I am using the most recent version of seqkit.

[shenwei356]

Would you please send the removed short sequence and the long one (or simply the whole file) to me, here or by email: shenwei356@gmail.com.

[shenwei356]

any update?