Spa typing quality score

The Ridom StaphType quality scores consists of 5 or 6 more or less heuristically defined quality categories and the exact method of determining the quality of a sequence is not publicly available. Instead of trying to reverse-engineer the criteria for these quality categories, we chose to implement a sequence quality score similar to Q20, a commonly used sequence quality measure, and is basically the percentage of bases in the contig that are covered by good-quality trace calls. In collaboration with SeqNet.org, we ran a comparison test on 200 Spa strains of varying quality and found a strong correlation between the StaphType and BioNumerics quality values, with a BN quality of 70% corresponding to the StaphType quality cutoff for submission to the SpaServer. However, there will always be border-line cases where a particular strain passes the quality test in one software package and not in the other. Actually, quite some strains passed the BioNumerics quality test and not the StaphType test when there was a large difference in the amplitudes between the forward and reverse traces, but this may have been fixed.