PHRED

Effects of sample re-sequencing and trimming on the quality and size of assembled consensus sequences

F. Prosdocimi, Lopes, D. A. O., Peixoto, F. C., Mourão, M. M., Pacífico, L. G. G., Ribeiro, R. A., and Ortega, J. M., “Effects of sample re-sequencing and trimming on the quality and size of assembled consensus sequences”, vol. 6, pp. 756-765, 2007.

The production of nucleic acid sequences by automatic DNA sequencer machines is always associated with some base-calling errors. In order to produce a high-quality DNA sequence from a molecule of interest, researchers normally sequence the same sample many times. Considering base-calling errors as rare events, re-sequencing the same molecule and assembling the reads produced are frequently thought to be a good way to generate reliable sequences.

Evaluation of window cohabitation of DNA sequencing errors and lowest PHRED quality values

F. Prosdocimi, Peixoto, F. Cruz, and Ortega, J. Miguel, “Evaluation of window cohabitation of DNA sequencing errors and lowest PHRED quality values”, vol. 3, pp. 483-492, 2004.

When analyzing sequencing reads, it is important to distinguish between putative correct and wrong bases. An open question is how a PHRED quality value is capable of identifying the miscalled bases and if there is a quality cutoff that allows mapping of most errors. Considering the fact that a low quality value does not necessarily indicate a miscalled position, we decided to investigate if window-based analyses of quality values might better predict errors.

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