We present PEACE, a stand-alone tool for high-throughput ab initio clustering of transcript fragment sequences produced by Next Generation or Sanger Sequencing technologies. It is freely available from www.peace-tools.org. Installed and managed through a downloadable user-friendly graphical user interface (GUI), PEACE can process large data sets of transcript fragments of length 50 bases or greater, grouping the fragments by gene associations with a sensitivity comparable to leading clustering tools. Once clustered, the user can employ the GUI's analysis functions, facilitating the easy collection of statistics and allowing them to single out specific clusters for more comprehensive study or assembly. Using a novel minimum spanning tree-based clustering method, PEACE is the equal of leading tools in the literature, with an interface making it accessible to any user. It produces results of quality virtually identical to those of the WCD tool when applied to Sanger sequences, significantly improved results over WCD and TGICL when applied to the products of Next Generation Sequencing Technology and significantly improved results over Cap3 in both cases. In short, PEACE provides an intuitive GUI and a feature-rich, parallel clustering engine that proves to be a valuable addition to the leading cDNA clustering tools.
PEACE and EAST, together forming a pipeline for the clustering and assembly of EST transcript fragments, make use of a novel 2 -based minimum spanning tree algorithm that results in quickly generated, high quality assemblies when applied to the results of Sanger sequencing. The tool is considerably more robust to sequencing error than competing assembly fragments, and has shown to be effective when applied to next generation technologies producing reads of moderate size (e.g. 454).
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