title: Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.
abstract: BACKGROUND
  High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein-DNA and protein-RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing.
  
  
  RESULTS
  We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics.
  
  
  BACKGROUND
  Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxy
  
  
  BACKGROUND
  eduardo.eyras@upf.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Universitat Pompeu Fabra, E08003 Barcelona, Spain.
authors: Sonja
authors: S
authors: Althammer
authors: Juan
authors: J
authors: González-Vallinas
authors: Cecilia
authors: C
authors: Ballaré
authors: Miguel
authors: M
authors: Beato
authors: Eduardo
authors: E
authors: Eyras
mesh_terms: D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods; D003201:Computers; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software