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Old 02-27-2010, 09:20 PM   #1
dina
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Default sff extract

Hi
How can I extract sff files? only in linux or windows is possible too?
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Old 02-28-2010, 01:47 AM   #2
rglover
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http://bioinf.comav.upv.es/sff_extract/
This program will do the job. It works on Windows and linux so long as you have python installed.
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Old 02-28-2010, 05:56 AM   #3
bio-x
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you can try:

Usage: sffinfo [options...] [- | sfffile] [accno...]
Options:
-a or -accno Output just the accessions
-s or -seq Output just the sequences
-q or -qual Output just the quality scores
-f or -flow Output just the flowgrams
-t or -tab Output the seq/qual/flow as tab-delimited lines
-n or -notrim Output the untrimmed sequence or quality scores
-m or -mft Output the manifest text
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Old 03-01-2010, 03:55 AM   #4
maubp
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bio-x is suggesting using the Roche tool sffinfo which comes with the "Newbler" package. Note that this is Linux only. See also getting Newbler.
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