Semiconductor sequencing: how many flows do you need?
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Semiconductor sequencing: how many flows do you need? / Budczies, Jan; Bockmayr, Michael; Treue, Denise; Klauschen, Frederick; Denkert, Carsten.
in: BIOINFORMATICS, Jahrgang 31, Nr. 8, 15.04.2015, S. 1199-203.Publikationen: SCORING: Beitrag in Fachzeitschrift/Zeitung › SCORING: Zeitschriftenaufsatz › Forschung › Begutachtung
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TY - JOUR
T1 - Semiconductor sequencing: how many flows do you need?
AU - Budczies, Jan
AU - Bockmayr, Michael
AU - Treue, Denise
AU - Klauschen, Frederick
AU - Denkert, Carsten
N1 - © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
PY - 2015/4/15
Y1 - 2015/4/15
N2 - MOTIVATION: Semiconductor sequencing directly translates chemically encoded information (A, C, G or T) into voltage signals that are detected by a semiconductor device. Changes of pH value and thereby of the electric potential in the reaction well are detected during strand synthesis from nucleotides provided in cyclic repeated flows for each type of nucleotide. To minimize time requirement and costs, it is necessary to know the number of flows that are required for complete coverage of the templates.RESULTS: We calculate the number of required flows in a random sequence model and present exact expressions for cumulative distribution function, expected value and variance. Additionally, we provide an algorithm to calculate the number of required flows for a concrete list of amplicons using a BED file of genomic positions as input. We apply the algorithm to calculate the number of flows that are required to cover six amplicon panels that are used for targeted sequencing in cancer research. The upper bounds obtained for the number of flows allow to enhance the instrument throughput from two chips to three chips per day for four of these panels.AVAILABILITY AND IMPLEMENTATION: The algorithm for calculation of the flows was implemented in R and is available as package ionflows from the CRAN repository.CONTACT: jan.budczies@charite.deSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
AB - MOTIVATION: Semiconductor sequencing directly translates chemically encoded information (A, C, G or T) into voltage signals that are detected by a semiconductor device. Changes of pH value and thereby of the electric potential in the reaction well are detected during strand synthesis from nucleotides provided in cyclic repeated flows for each type of nucleotide. To minimize time requirement and costs, it is necessary to know the number of flows that are required for complete coverage of the templates.RESULTS: We calculate the number of required flows in a random sequence model and present exact expressions for cumulative distribution function, expected value and variance. Additionally, we provide an algorithm to calculate the number of required flows for a concrete list of amplicons using a BED file of genomic positions as input. We apply the algorithm to calculate the number of flows that are required to cover six amplicon panels that are used for targeted sequencing in cancer research. The upper bounds obtained for the number of flows allow to enhance the instrument throughput from two chips to three chips per day for four of these panels.AVAILABILITY AND IMPLEMENTATION: The algorithm for calculation of the flows was implemented in R and is available as package ionflows from the CRAN repository.CONTACT: jan.budczies@charite.deSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
KW - Algorithms
KW - Genome, Human
KW - Genomics
KW - High-Throughput Nucleotide Sequencing
KW - Humans
KW - Neoplasms
KW - Semiconductors
KW - Sequence Analysis, DNA
KW - Software
KW - Journal Article
KW - Research Support, Non-U.S. Gov't
U2 - 10.1093/bioinformatics/btu805
DO - 10.1093/bioinformatics/btu805
M3 - SCORING: Journal article
C2 - 25480372
VL - 31
SP - 1199
EP - 1203
JO - BIOINFORMATICS
JF - BIOINFORMATICS
SN - 1367-4803
IS - 8
ER -