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Copy Number Analysis for Targeted Resequencing (CONTRA) is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
Tools to select sequences for capture enrichment of next-gen libraries
...These sequences are used as a query during a BLAST search of the unannotated genome of a non-model species, and then the corresponding sequences are returned, which can be used to design baits for hybridization-based sequence capture.