Remove A List of Sequences from the MSA File

Question

[Tastulek]

Hello Everyone,

I have an MSA file containing hundreds of sequences aligned by BWA. Now I would like to remove a list of sequences from the MSA file, is there a quick way to do this? or Could the MSA file be split into two?!

I would appreciate your response!

Answer 1

[atorreso]

You can prepare a list with the sequences you want to keep (so the reverse of the sequences you want to remove) and use seqtk. As explained in their github (https://github.com/lh3/seqtk):

 seqtk subseq in.fq name.lst > out.fq

[Tastulek]

atorreso Thank you so much!