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
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author Hyman, Richard W
Jiang, Hui
Fukushima, Marilyn
Davis, Ronald W
author_facet Hyman, Richard W
Jiang, Hui
Fukushima, Marilyn
Davis, Ronald W
author_sort Hyman, Richard W
collection PubMed
description 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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spelling pubmed-30206622011-01-14 A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry Hyman, Richard W Jiang, Hui Fukushima, Marilyn Davis, Ronald W BMC Res Notes Research Article 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. BioMed Central 2010-10-08 /pmc/articles/PMC3020662/ /pubmed/20932319 http://dx.doi.org/10.1186/1756-0500-3-257 Text en Copyright ©2010 Hyman et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Hyman, Richard W
Jiang, Hui
Fukushima, Marilyn
Davis, Ronald W
A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry
title A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry
title_full A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry
title_fullStr A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry
title_full_unstemmed A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry
title_short A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry
title_sort direct comparison of the kb™ basecaller and phred for identifying the bases from dna sequencing using chain termination chemistry
topic Research Article
url 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
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