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Maximum PHRED score

About this program

This program is a sister program to RegionOfInterest.exe and was produced as a second way of measuring the quality of DNA sequences created on an ABI sequencer. This data was then used to compare the quality of the sequence to the rate of false positives and negatives of a program I was writing.

Like RegionOfInterest.exe the program uses the ABI (*.phd.1) files generated by the ABI base caller. However it differs in that the user supplies a length value and the program calculates the maximum average Phred score for a stretch of DNA of that length. The position of this sequence can differ from one file to another and is just a general quality score for a file.

The program asks for a cut off value, if the average Phred value is lower than this the sequence it is said to have failed quality control. Similarly, if the sequence is shorter than the search length trace file is deemed to have failed.

The program analyses all the files in a folder and creates an output file that that contains the average Phred scores for the alignment and a summary of whether the sequence passes the quality control steps.

For short description on how the Phred scores are calculated look here.

insilicase icon This program can be downloaded here.

10 quality files and a text file containing the sequence of the region of interest can be downloaded here. These sequences contain a number of sequence variants that are reported as 'N'.

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