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TADtool: visual parameter identification for TAD-calling algorithms

Author:
Kruse, Kai, Hug, Clemens B., Hernández-Rodríguez, Benjamín, Vaquerizas, Juan M.
Source:
Bioinformatics 2016 v.32 no.20 pp. 3190-3192
ISSN:
1460-2059
Subject:
algorithms, bioinformatics, computer software, genome
Abstract:
Summary: 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. Availability and implementation: 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). Contact: kai.kruse@mpi-muenster.mpg.de, jmv@mpi-muenster.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.
Agid:
6247457