TADtool: visual parameter identification for TAD-calling algorithms.
Eukaryotic genomes are hierarchically organized into topologically associating domains (TADs). The computational identification of these domains and their associated properties critically depends on the choice of suitable parameters of TAD-calling algorithms. To reduce the element of trial-and-error in parameter selection, we have developed TADtool: an interactive plot to find robust TAD-calling parameters with immediate visual feedback. TADtool allows the direct export of TADs called with a chosen set of parameters for two of the most common TAD calling algorithms: directionality and insulation index. It can be used as an intuitive, standalone application or as a Python package for maximum flexibility.



TADtool is available as a Python package from GitHub (https://github.com/vaquerizaslab/tadtool) or can be installed directly via PyPI, the Python package index (tadtool).



kai.kruse@mpi-muenster.mpg.de, jmv@mpi-muenster.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.
Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany.
Kai
K
Kruse
Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany.
Clemens B
CB
Hug
Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany.
Benjamín
B
Hernández-Rodríguez
Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany.
Juan M
JM
Vaquerizas
D000465:Algorithms; D000818:Animals; D016678:Genome; D006801:Humans; D012984:Software