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--- archive:computer_resources:sff_extract [2010/04/24 08:57]
mpcusack created
+++ archive:computer_resources:sff_extract [2015/09/02 16:34] (current)
ceisenhart ↷ Page moved from computer_resources:sff_extract to archive:computer_resources:sff_extract
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 ====== sff_extract ======
-[[http://bioinf.comav.upv.es/sff_extract/index.html|sff_extract]] is a utility from the [[http://www.comav.upv.es/|Center for the Conservation and Breeding of the Agrodiverdity]] at the Polythechnical University of Valencia
+[[http://bioinf.comav.upv.es/sff_extract/index.html|sff_extract]] is a utility from the [[http://www.comav.upv.es/|Center for the Conservation and Breeding of the Agrodiverdity]] at the Polythechnical University of Valencia.
+produces data in a binary sff format. Most assemblers (other than newbler) don't read sff directly. Instead they require fasta and fasta.qual data. This software produces both of these as well as a xml file containing clipping information. It can be fed with multiple sff files and produce a single fasta file.
+It seems that sff_extract overlaps in functionality with the Roche-provided sffinfo tool.  It is not clear what (if any) advantage there is to the sff_extract tool.  I suspect that sffinfo may do a better job of converting flow-space to base space. --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/04/24 07:59//

Banana Slug Genomics