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WiggleTools specifications


Unique identifier OMICS_02188
Name WiggleTools
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Python
License Apache License version 2.0
Computer skills Medium
Version 1.2.2
Stability Stable
LibBigWig, HTSLib, GSL
Maintained Yes



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  • person_outline Paul Flicek <>
  • person_outline Daniel Zerbino <>

Publication for WiggleTools

WiggleTools in publications

PMCID: 5863514
PMID: 29599703
DOI: 10.3389/fnins.2018.00119

[…] pearson's correlation on the two replicates calculated with a call to wigcorrelate (http://hgdownload.soe.ucsc.edu/admin/exe/macosx.x86_64/) or wiggletools (zerbino et al., ) gave a value of 0.9. peaks were annotated based on nearest transcription start site (tss) using the bioconductor package chippeakanno (zhu et al., ) and chipseeker (yu […]

PMCID: 5511350
PMID: 28703137
DOI: 10.1038/ncomms16058

[…] normalized genome-wide signal per histone modification per cell type in bigwig format using align2rawsignal (https://github.com/akundaje/align2rawsignal) on two biological replicates. then we used wiggletools to count the mean number of reads per 200 bp bins across the genome. finally, ideas identified 30 distinct states that were used to classify each 200 bp bin across genome in both cell […]

PMCID: 5120258
PMID: 27876760
DOI: 10.1038/srep37393

[…] distances where then intersected with the “primary b cells from cord blood” chromatin state segmentation using bigwigaverageoverbed, discarding segments with less than three covered cpgs. we used wiggletools to average the dna methylation rates of the medulloblastoma data set (icgc:pbca-de) for the four distinct cancer groups group3, group4, shh and wnt, and the control set. we also used […]

PMCID: 4667523
PMID: 26633995
DOI: 10.1186/s13072-015-0046-0

[…] files were smoothed using the jgk gaussiansmooth tool with standard deviation of 20 bp. motif analyses were performed using haystack []. area-under-the-curve measurements were performed using the wiggletools package []. gene ontology analyses were performed using the great package []., k-means clustering was performed using the computematrix and heatmapper functions of deeptools []. we first […]

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WiggleTools institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
WiggleTools funding source(s)
Supported by The Wellcome Trust (WT095908) and EMBL; and by the European Union’s Seventh Framework Programme (FP7/2007- 2013) under grant agreement n 282510-BLUEPRINT.

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