USeq is a collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations.
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Nix DA, Courdy SJ, Boucher KM:
Empirical methods for controlling false positives and estimating confidence in chIP-seq peaks.
BMC Bioinformatics. 2008 Dec 5;9(1):523.