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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 files. Phred is not included as part of the Staden Package. It is available from Phil Green. There are no adjustable parameters for this module.

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.