Phred is an ABI base caller. Ewing, B. and Green, P. 1998. Base-Calling
of Automated Sequencer Traces Using Phred. II. Error Probabilities. Genome
Res. 8, 186-194. It will analyse the chromatogram data to produce new base
calls. For each base it assigns confidence value indicating how likely this
base call is to be correct. These confidence values are significantly more
reliable than those produced by eba and they are compatible with the Phrap
assembly program and the Gap4 consensus algorithm.
Phred can process either ABI or SCF files. It should be possible to run it on
ALF files by firstly ensuring that the ALF/ABI to SCF Conversion module has
been run, however the performance of Phred has been specifically tuned to ABI
files and we do not know how reliable it will be operating on converted ALF
Phred is not included as part of the Staden Package. It is available from Phil
There are no adjustable parameters for this module.
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Last generated on 2 Febuary 1999.