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  • konika
    Member
    • Sep 2010
    • 14

    #1

    Identifying the type of sequencing from a SFF file

    Hi
    I have a very basic question,
    I have a .SFF file. I know its not paired end reads data, but I was wondering how can I get more information from it such as : which type of sequencing is it?
    After reading the file in R I could locate
    [[1]]$header_length
    [1] 840
    #840 stands for GS FLX Titanium reads, but doesn't say if is it is paired end or something else etc.
    Hope someone can help.
    Thanks
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    Give Flower a try: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065695/

    Comment

    • maubp
      Peter (Biopython etc)
      • Jul 2009
      • 1544

      #3
      You can use the sffinfo tool from the Roche "off instrument" suite (search for how to download "Newbler").

      You could also use Biopython's SFF parser and look at the annotation of any of the reads, e.g.

      Code:
      from Bio import SeqIO
      record = next(SeqIO.parse("my_file.sff", "sff"))
      print(len(record.annotations["flow_chars"]))
      e.g. 400 flow cycles for the example I just used.

      Comment

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