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Uses multiple tools to identify peaks. SigSeeker works about existing peak comparisons by including peak overlaps of varying minimal width and peak-intensity correlation models. This is done to refine peak predictions in an unsupervised approach. It combines positional and quantitative filtering as part of a peak-calling ensemble. This tool can be used with any peak-calling approach whose input (1) consists of aligned sequencing reads in the BED file format or (2) is in a form that can be converted to BED (e.g. SAM, BAM, ELAND) and that generates peak lists in BED or compatible formats.

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SigSeeker classification

SigSeeker specifications

Application programming interface
Programming languages:
Restrictions to use:
Computer skills:

SigSeeker support



  • Jens Lichtenberg <>

Additional information

The SigSeeker code is available from:


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Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Rockville, MD, USA

Funding source(s)

This work was supported by National Human Genome Research Institute intramural funds.

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