CRAC is designed to find splice junctions, fusion junctions, SNVs, indels in reads. It focuses on the unique location of a read. It performs particularly well on long reads. It is designed for resequencing projects and is therefore able to map reads coming from the same species or a close one.
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Genome Biol. 2013 Mar 28;14(3):R30.
CRAC: an integrated approach to the analysis of RNA-seq reads.
Philippe N, Salson M, Commes T, Rivals E.