TADtool: visual parameter identification for TAD-calling algorithms.

ABSTRACT: 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] information: Supplementary data are available at Bioinformatics online.

SUBMITTER: Kruse K 

PROVIDER: S-EPMC5048066 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature