TADtool: visual parameter identification for TAD-calling algorithms

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: [e-mail], [e-mail]
Supplementary information: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics - October 2, 2016 Category: Bioinformatics Authors: Kruse, K., Hug, C. B., Hernandez-Rodriguez, B., Vaquerizas, J. M. Tags: GENOME ANALYSIS Source Type: research