NucTools protocols

View NucTools computational protocol

NucTools statistics

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Associated diseases

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NucTools specifications


Unique identifier OMICS_16871
Name NucTools
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data A raw DNA read.
Input format BED
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Medium
Version 2.0
Stability Stable
Maintained Yes



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  • person_outline Yevhen Vainshtein <>

Publication for NucTools

NucTools in pipeline

PMCID: 5403151
PMID: 28406749
DOI: 10.1080/19491034.2017.1295201

[…] 160 bp, 159 bp and 159 bp, reflecting a moderate chromatin digestion (in a strongly digested chromatin dna fragments are closer to the 147bp nucleosome dna length). mapped reads were processed using nuctools to generate genome-wide nucleosome occupancy landscapes, extract individual genomic regions and calculate nrl, as described previously. aggregate nucleosome occupancy profiles around genomic […]

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NucTools in publication

PMCID: 5403151
PMID: 28406749
DOI: 10.1080/19491034.2017.1295201

[…] and nucleosome repositioning take place upon hl-60/s4 cells differentiation into granulocyte (ra-treated) or macrophage (tpa-treated) cell forms. using a “sliding window” approach with the help of nuctools software, we defined 1000-bp genomic regions which are characterized by significant loss or gain of nucleosome occupancy upon differentiation with ra or tpa (see methods). we have identified […]

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NucTools institution(s)
Functional Genomics Group, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany; Research Group Genome Organization & Function, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany; School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
NucTools funding source(s)
Supported by the intramural grant “Developing a software suite for the analysis of epigenetic regulation from high-throughput sequencing data” within the cross-topic program [email protected] at the German Cancer Research Center, as well as the Wellcome Trust grant 200733/Z/16/Z.

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