phred is an algorithm that takes chromatogram information from an automated sequencing run and re-evaluates the peaks to produce a “base call” that is usually significantly more accurate than the original call. In addition to recalculating the residues, phred also adds quality score information to each residue. This is a logarithmic value from 0 to 99 where a value of 10 indicates that there is a 1 in 10 chance that the call is in error, a score of 20 indicates in 1 in 100 chance the call is in error, a score of 30 indicates a 1 in 1,000 chance of an error etc. MacVector Assembler takes advantage of multi core machines and splits up the phred jobs between the processors so that you see a speed up directly proportional to the number of processors. In addition, the phred executable is a Universal Binary, so it runs at full native speed. Once you have basecalled the imported sequences, you can view the phred base calls and the quality values by double-clicking on one of the sequences.
