Phred

Phred is not included as part of the Staden Package. It is available from Phil Green. http://www.genome.washington.edu/UWGC/analysistools/phred.htm

Description

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, but pregap4 will automatically convert all input to SCF format first. This means that the phred pregap4 module will be able to process any supported trace format.

There are no adjustable parameters for this module.