Pyicos – a powerful toolkit for the analysis of mapped reads

Pyicos is 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.

AVAILABILITY: Open source software, with tutorials and protocol-files, is available at or as a Galaxy server at

  • Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E. (2011) Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics [Epub ahead of print]. [abstract]