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Old 08-04-2009, 07:08 PM   #3
Senior Member
Location: The University of Melbourne, AUSTRALIA

Join Date: Apr 2008
Posts: 275

I just use the "sffinfo" tool that 454 distribute.

sffinfo -s file.sff > file.fasta
sffinfo -q file.sff > file.qual
sffinfo -m file.sff > file.manifest.xml

Here is the usage:

Usage: sffinfo [options...] [- | sfffile] [accno...]
-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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