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LUCY is the program for DNA sequence quality trimming and vector removal. It was designed to take the base-call quality assessment of each base into consideration in the cleaning process, to make sure the processed sequences have the best overall quality possible based on their individual base quality value. Lucy's task is to identify the largest subsequence that is of sufficiently high quality and also free of contaminating vector sequence.
To run this software interactively in a Linux environment run the commands:
module load lucy lucy -v PUC19 PUC19splice atie.seq atie.qul atie.2nd -debug lucy.info
Home Page: http://sourceforge.net/projects/lucy
Lucy is fully described in: DNA sequence quality trimming and vector removal. H.-H. Chou and M.H. Holmes.Bioinformatics , 17:12, pp. 1093-1104, 2001 manpage available.