I have sff files from 454 sequencing. How do I convert sff to fasta or fastq format?
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How to convert from sff to fasta or fastq
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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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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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this program works very well for converting directly from sff to fastq
http://indraniel.wordpress.com/2010/04/23/sff2fastq/
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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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