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How to convert from sff to fasta or fastq

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  • How to convert from sff to fasta or fastq

    I have sff files from 454 sequencing. How do I convert sff to fasta or fastq format?

  • #2
    See this thread:

    http://seqanswers.com/forums/showthread.php?t=2775

    Chris

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    • #3
      There is a roche script called "sffinfo", which takes and sff file and generate a fasta file.

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      • #4
        Yes, both sffinfo from Roche and the free open source options of sff_extract and Biopython were mentioned in the thread Chris linked to:
        http://seqanswers.com/forums/showthread.php?t=2775

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        • #5
          I've converted sff to fastq using sffinfo to generate the fasta and qual files. You can then combine them using the perl script on this page
          http://seqanswers.com/forums/showthr...sta+qual+fastq
          to combine them into Sanger fastq. Your fasta and qual files should have the same basename for it to work.

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          • #6
            Originally posted by TonyBrooks View Post
            I've converted sff to fastq using sffinfo to generate the fasta and qual files. You can then combine them using the perl script on this page
            "sff_extract -Q" seems easier in handling :-)

            B.

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            • #7
              You can simply type the command below and it will generate 3 files, .fasta, .fasta.qual, .xml, for you.

              sff_extract XXX.sff

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              • #8
                Does this sff_extract can handle multiplex files? I have 48individuals/run on a Roche 454 junior and I would like to demultiplex the sff files.

                Thanks.

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                • #9
                  I don't think sff_extract can do this (yet). Assuming you are using the standard Roche 454 MID barcodes, then Roche's sfffile from their "off instrument applications" package would be the easiest way to do this.

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                  • #10
                    this program works very well for converting directly from sff to fastq

                    http://indraniel.wordpress.com/2010/04/23/sff2fastq/

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                    • #11
                      Using Biopieces you can do:

                      Code:
                      read_sff -i data.sff | write_fastq -o data.fq -x
                      or

                      Code:
                      read_sff -i data.sff | write_454 -o data.fna -q data.fna.qual -x
                      or both in one go:

                      Code:
                      read_sff -i data.sff | write_fastq -o data.fq | write_454 -o data.fna -q data.fna.qual -x

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                      • #12
                        Originally posted by maasha View Post
                        Using Biopieces you can do:
                        Thank you - discovered Biopieces because of this post and, after some mucking around with macports and ruby installations on OSX, finally got it working. THANK YOU. Very handy set up tools.
                        @bioinformer
                        http://www.linkedin.com/in/jonathanjacobs

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                        • #13
                          I am building a tool with graphical interface that will convert SFF to FASTQ and multifasta.
                          Last edited by create.share; 06-03-2014, 01:11 AM.

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