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Updated: Jun 8, 2026

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
Published on: June 19, 2018
A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain
Richard W Hyman1, Hui Jiang, Marilyn Fukushima
1Stanford Genome Technology Centre, 855 S, California St,, Palo Alto, CA 94304, USA. rhyman@stanford.edu.
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.
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