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PARA-suite / PAR-CLIP analyzer suite
A toolkit for processing and aligning short and error-prone sequencing reads. PARA-suite is implemented in Java using HTSjdk, a Java API for high-throughput sequencing data formats. The PARA-suite allows the user to estimate a sequencing run-specific error profile, combine the results of multiple reference database alignments, cluster an aligned sequencing read dataset (‘PAR-CLIP read simulator and hierarchical clustering’), run the PAR-CLIP read simulator, benchmark an alignment of simulated PAR-CLIP sequencing reads and run a full processing pipeline for error-prone short read alignments.
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