[Bioperl-l] SCF files

Alexander Kozik akozik at atgc.org
Fri Nov 3 17:29:49 EST 2006


Hi all,

There is a contradiction in opinions (I have used google search) what 
type of data SCF files (sequencing chromatograms) carry. Could you help 
to clarify following topics:

are these statements true or false:

1. SCF files can be generated by Phred program only.

2. new version of Phred can read SCF files produced by older version of 
Phred and re-do basecalling with new quality scores [new quality scores 
could be different because of the improvements/changes in a basecalling 
algorithm]

3. SCF files contain no less information as original AB1 files [in other 
words, no information lost during conversion of AB1 to SCF]

Thanks,

-Alex

========================================

Alexander Kozik
Bioinformatics Specialist
Genome and Biomedical Sciences Facility
451 East Health Sciences Drive
University of California
Davis, CA 95616-8816
Phone: (530) 754-9127
email: akozik at atgc.org
web: http://www.atgc.org/

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