split sff files

Hi everyone,
I don’t know if it is possible, but I would like to plit my general sff into small sff files sorresponding to each MID in order to submit them to the GenBank. My general sff contains data which is not form my study, so I can not simply cut the sff. Can I do this with mothur??


I need the opposite - my sequencing center sometimes provides samles from the same experiment in different SFF siles, and I’d love a way to merge them and analyze all at once.


Hello peleliu,

My sampling facility does the same thing, so I have to merge my samples using the merge.files command. If you go to the link below, you can see how I did it after extracting the fasta, names and groups file using the sffinfo command.

Hope this helps! :slight_smile:


Thanks Tamar!

  1. Why won’t you merge the files right after the sffinfo?
  2. you can further streamline your workflow by doing:
    mothur > sffinfo(sff=fileA-fileB-fileC-fileD)


Oh because I wanted the FASTA file so that I could be sure that my sequencing facility gave me the correct barcode sequences for each sample and that I successfully removed them, as well as my primer sequences, before I merged.