Phred quality score

[1][2] It was originally developed for the computer program Phred to help in the automation of DNA sequencing in the Human Genome Project.

Phred quality scores are assigned to each nucleotide base call in automated sequencer traces.

Perhaps the most important use of Phred quality scores is the automatic determination of accurate, quality-based consensus sequences.

The idea of sequence quality scores can be traced back to the original description of the SCF file format by Rodger Staden's group in 1992.

In contrast, instrument manufacturers like ABI continued to adapt their base calling software changes in sequencing chemistry, and have included the ability to create Phred-like quality scores.

Therefore, the need to use Phred for base calling of DNA sequencing traces has diminished, and using the manufacturer's current software versions can often give more accurate results.

Within the Human Genome Project, the most important use of Phred quality scores was for automatic determination of consensus sequences.

Phrap's use of Phred quality scores effectively automated finding the highest-quality consensus sequence; in most cases, this completely circumvents the need for any manual editing.

For example, the algorithm QualComp[9] performs lossy compression with a rate (number of bits per quality value) specified by the user.

Based on rate-distortion theory results, it allocates the number of bits so as to minimize the MSE (mean squared error) between the original (uncompressed) and the reconstructed (after compression) quality values.

Other algorithms for compression of quality values include SCALCE,[10] Fastqz[11] and more recently QVZ,[12] AQUa[13] and the MPEG-G standard, that is currently under development by the MPEG standardisation working group.

For example, SCALCE reduces the alphabet size based on the observation that “neighboring” quality values are similar in general.