title: Semiconductor sequencing: how many flows do you need?
abstract: BACKGROUND
  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.
  
  
  METHODS
  The algorithm for calculation of the flows was implemented in R and is available as package ionflows from the CRAN repository.
  
  
  BACKGROUND
  jan.budczies@charite.de
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Budczies
authors.affiliation: Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Bockmayr
authors.affiliation: Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany.
authors.forename: Denise
authors.initials: D
authors.lastname: Treue
authors.affiliation: Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany.
authors.forename: Frederick
authors.initials: F
authors.lastname: Klauschen
authors.affiliation: Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany Institute of Pathology, Charité University Hospital, Charitéplatz 1, 10117 Berlin, Germany, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and German Consortium for Translational Cancer Research (DKTK), Berlin partner site, Charitéplatz 1, 10117 Berlin, Germany.
authors.forename: Carsten
authors.initials: C
authors.lastname: Denkert
mesh_terms: D000465:Algorithms; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D012666:Semiconductors; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software