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How to convert from sff to fasta or fastq

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  • create.share
    replied
    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.

    Leave a comment:


  • jonathanjacobs
    replied
    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.

    Leave a comment:


  • maasha
    replied
    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

    Leave a comment:


  • empyrean
    replied
    this program works very well for converting directly from sff to fastq

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

    Leave a comment:


  • maubp
    replied
    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.

    Leave a comment:


  • fadista
    replied
    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.

    Leave a comment:


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

    sff_extract XXX.sff

    Leave a comment:


  • BaCh
    replied
    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.

    Leave a comment:


  • TonyBrooks
    replied
    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.

    Leave a comment:


  • maubp
    replied
    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

    Leave a comment:


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

    Leave a comment:


  • cjp
    replied
    See this thread:

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

    Chris

    Leave a comment:


  • shuang
    started a topic How to convert from sff to fasta or fastq

    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?

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