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Summary: The NARWHAL software pipeline has been developed to automate the primary analysis of Illumina sequencing data. This pipeline combines a new and flexible de-multiplexing tool with open-source aligners and automated quality assessment. The entire pipeline can be run using only one simple sample-sheet for diverse sequencing applications. NARWHAL creates a sample-oriented data structure and outperforms existing tools in speed. Availability: https://trac.nbic.nl/narwhal/ Contact: w.vanijcken@erasmusmc.nl Supplementary information: Supplementary data are available at Bioinformatics online.
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Brouwer et al. (2011) studied this question.
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