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Old 11-29-2011, 11:05 AM   #1
shuang
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Default 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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Old 11-29-2011, 11:10 AM   #2
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See this thread:

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

Chris
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Old 11-29-2011, 06:38 PM   #3
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There is a roche script called "sffinfo", which takes and sff file and generate a fasta file.
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Old 11-30-2011, 07:48 AM   #4
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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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Old 11-30-2011, 08:14 AM   #5
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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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Old 12-01-2011, 04:26 AM   #6
BaCh
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Quote:
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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Old 12-02-2011, 08:33 AM   #7
shuang
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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.sff
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Old 12-16-2011, 03:06 AM   #8
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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.
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Old 12-16-2011, 03:50 AM   #9
maubp
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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.
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Old 12-16-2011, 12:16 PM   #10
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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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Old 01-18-2012, 03:13 AM   #11
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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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Old 07-11-2012, 10:03 AM   #12
jonathanjacobs
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Quote:
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.
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Old 05-15-2014, 09:09 AM   #13
create.share
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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 at 02:11 AM.
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