I have an output from Bbduk that are single unpaired reads that have both R1/R2 in them, NOT interleaved. Is there a program that I can use to separate the R1 and R2 into different files?
Hi @Jon_Colman
Yes, this is definitely possible!
seqtk_seq should work fine. If you haven’t tried that yet, please do. If you run into problems, I can suggest more complicated alternatives, and seeing your error message and a few of the sequences would be helpful (both forward and reverse). A shared history would be ideal.
Thanks! 