title: KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis.
abstract: Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis. We also describe important technical extensions. The high throughput executor (HTE) helps to increase the reliability and to reduce manual interventions when processing complex datasets. We also provide a dedicated binary manager that assists users in obtaining the modules' executables and keeping them up to date. As basis for this actively developed toolbox we use the workflow management software KNIME.
  
  
  
  See http://ibisngs.github.io/knime4ngs for nodes and user manual (GPLv3 license).
  
  
  
  robert.kueffner@helmholtz-muenchen.de.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Maximilian
authors.initials: M
authors.lastname: Hastreiter
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Tim
authors.initials: T
authors.lastname: Jeske
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hoser
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Kluge
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Kaarin
authors.initials: K
authors.lastname: Ahomaa
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Marie-Sophie
authors.initials: MS
authors.lastname: Friedl
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Sebastian J
authors.initials: SJ
authors.lastname: Kopetzky
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Jan-Dominik
authors.initials: JD
authors.lastname: Quell
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: H-Werner
authors.initials: HW
authors.lastname: Mewes
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Robert
authors.initials: R
authors.lastname: Küffner
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D057188:Workflow