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

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...

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Detalles Bibliográficos
Autores principales: Hyman, Richard W, Jiang, Hui, Fukushima, Marilyn, Davis, Ronald W
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020662/
https://www.ncbi.nlm.nih.gov/pubmed/20932319
http://dx.doi.org/10.1186/1756-0500-3-257
Descripción
Sumario: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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