Filter sequences by dust score and entropy

[fgvieira]

Would it be possible to add to seqkit seq options to filter sequences by dust score and entropy. It would be similar to Prinseq and FastP.

[shenwei356]

Sorry, I forgot this. Do you want to filter sequences of low-complexity? but usually, they are only parts of a larger sequence.

[fgvieira]

Yes, the idea would be to remove the ones with ow complexity.

[shenwei356]

With any low-complexity region or the whole sequence is of low-complexity? And how long are these sequences?

[fgvieira]

Finding low-complexity region would be a nice feature, but it would be more complicated to implement and not sure how useful it would actually be (would you throw away the whole seq if there is a 30bp TA repeat?).

So, for now, I'd say, if the whole sequence is low-complexity.