Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering

BACKGROUND: Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed. RESULTS: We propose a new peak-caller called ‘Sierra Platinum’ that allows peak-calling of replicated ChIP-seq experiments. Moreover, it provides a variety of quality measures together with integrated visualizations supporting the assessment of the replicates and the resulting peaks, as well as steering the peak-calling process. CONCLUSION: We show that Sierra Platinum outperforms currently available methods using a newly generated benchmark data set and using real data from the NIH Roadmap Epigenomics Project. It is robust against noisy replicates. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1248-6) contains supplementary material, which is available to authorized users.