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Open Access Research article

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

Richard W Hyman12*, Hui Jiang13, Marilyn Fukushima12 and Ronald W Davis124

Author Affiliations

1 Stanford Genome Technology Centre, 855 S. California St., Palo Alto, CA 94304, USA

2 Department of Biochemistry, Stanford University Medical School, Stanford, CA 94305, USA

3 Department of Statistics, Stanford University, Stanford, CA 94305, USA

4 Department of Genetics, Stanford University, Stanford, CA 94305, USA

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BMC Research Notes 2010, 3:257  doi:10.1186/1756-0500-3-257

Published: 8 October 2010



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.


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.


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.