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Semiconductor sequencing: how many flows do you need?

Standard

Semiconductor sequencing: how many flows do you need? / Budczies, Jan; Bockmayr, Michael; Treue, Denise; Klauschen, Frederick; Denkert, Carsten.

In: BIOINFORMATICS, Vol. 31, No. 8, 15.04.2015, p. 1199-203.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Budczies, J, Bockmayr, M, Treue, D, Klauschen, F & Denkert, C 2015, 'Semiconductor sequencing: how many flows do you need?', BIOINFORMATICS, vol. 31, no. 8, pp. 1199-203. https://doi.org/10.1093/bioinformatics/btu805

APA

Budczies, J., Bockmayr, M., Treue, D., Klauschen, F., & Denkert, C. (2015). Semiconductor sequencing: how many flows do you need? BIOINFORMATICS, 31(8), 1199-203. https://doi.org/10.1093/bioinformatics/btu805

Vancouver

Budczies J, Bockmayr M, Treue D, Klauschen F, Denkert C. Semiconductor sequencing: how many flows do you need? BIOINFORMATICS. 2015 Apr 15;31(8):1199-203. https://doi.org/10.1093/bioinformatics/btu805

Bibtex

@article{f78981d6f99a40d694fa08863bcfc1bb,
title = "Semiconductor sequencing: how many flows do you need?",
abstract = "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.",
keywords = "Algorithms, Genome, Human, Genomics, High-Throughput Nucleotide Sequencing, Humans, Neoplasms, Semiconductors, Sequence Analysis, DNA, Software, Journal Article, Research Support, Non-U.S. Gov't",
author = "Jan Budczies and Michael Bockmayr and Denise Treue and Frederick Klauschen and Carsten Denkert",
note = "{\textcopyright} The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.",
year = "2015",
month = apr,
day = "15",
doi = "10.1093/bioinformatics/btu805",
language = "English",
volume = "31",
pages = "1199--203",
journal = "BIOINFORMATICS",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "8",

}

RIS

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 -