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I have sff files from 454 sequencing. How do I convert sff to fasta or fastq format?
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See this thread:
Chris -
There is a roche script called "sffinfo", which takes and sff file and generate a fasta file.Comment
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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:
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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
to combine them into Sanger fastq. Your fasta and qual files should have the same basename for it to work.Comment
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You can simply type the command below and it will generate 3 files, .fasta, .fasta.qual, .xml, for you.
sff_extract XXX.sffComment
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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.Comment
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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.Comment
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this program works very well for converting directly from sff to fastq
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Using Biopieces you can do:
orCode:read_sff -i data.sff | write_fastq -o data.fq -x
or both in one go:Code:read_sff -i data.sff | write_454 -o data.fna -q data.fna.qual -x
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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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.Originally posted by maasha View PostComment
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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.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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