A recent paper presents the ChIP-seq analysis tool available in CLC Genomics Workbench and CLC Genomics Server (version 7.5 and later).
State-of-the-art peak calling algorithm
Some of the main requirements for the development of our peak calling toolset were generality, specificity, robustness, and simplicity. This resulted in the CLC shape-based peak caller which implements all the steps of signal detection, quality control, normalisation, discovering obvious peaks, learning the peak shape, peak shape score, and peak detection in a single, easy-to-use algorithm. The algorithm delivers a QC report containing metrics about the quality of the ChIP-seq experiment, a peak shape score value for every genomic position, and a list of all called peaks.
Performance
We have showed from a performance evaluation that the CLC shape-based peak caller ranks well among popular state-of-the-art peak callers while requiring a minimum of intervention and parameterization from the user.
Read the whole article: Identifying peaks in *-seq data using shape information (Lappe and Strino, 2016)
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