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Background  Relatively recently, the software KB™ Basecaller has replaced  phred  for identifying the bases from raw sequence data in DNA sequencing employing dideoxy chemistry. We have measured quantitatively the consequences of that change.    Results  The high quality sequence segment of reads derived from the KB™ Basecaller were, on average, 30-to-50 bases longer than reads derived from  phred . However, microbe identification appeared to have been unaffected by the change in software.    Conclusions  We have demonstrated a modest, but statistically significant, superiority in high quality read length of the KB™ Basecaller compared to  phred . We found no statistically significant difference between the numbers of microbial species identified from the sequence data.

A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry