Introduction

MOTIVATION: Although peak finding in next-generation sequencing (NGS) datasets has been addressed extensively, there is no consensus on how to analyze and process biological replicates. Furthermore, most peak finders do not focus on accurate determination of enrichment site widths and are not widely applicable to different types of datasets. RESULTS: We developed JAMM (Joint Analysis of NGS replicates via Mixture Model clustering): a peak finder that can integrate information from biological replicates, determine enrichment site widths accurately and resolve neighboring narrow peaks. JAMM is a universal peak finder that is applicable to different types of datasets. We show that JAMM is among the best performing peak finders in terms of site detection accuracy and in terms of accurate determination of enrichment sites widths. In addition, JAMM's replicate integration improves peak spatial resolution, sorting and peak finding accuracy. AVAILABILITY AND IMPLEMENTATION: JAMM is available for free and can run on Linux machines through the command line: http://code.google.com/p/jamm-peak-finder.

Publications

  1. JAMM: a peak finder for joint analysis of NGS replicates.
    Cite this
    Ibrahim MM, Lacadie SA, Ohler U, 2015-01-01 - Bioinformatics (Oxford, England)

Credits

  1. Mahmoud M Ibrahim
    Developer

    Department of Biology, Humboldt University, Germany

  2. Scott A Lacadie
    Developer

    Department of Biology, Humboldt University, Germany

  3. Uwe Ohler
    Investigator

    Department of Biology, Humboldt University, Germany

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Summary
AccessionBT006869
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByUwe Ohler