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All Firefly versions can take optional command line arguments. ... firefly [optional command line options in any order] [optional list of working directories] . ... The list of most widely used command line options is given below: . ... Disables validity check of the command line arguments (e.g., check for valid names of files and directories, etc...) passed to Firefly. ... However, if this option is not given, one must provide the list of working directories when running Firefly in parallel mode. ...

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Detection of short size mutations and copy number alterations in ultra-deep targeted sequencing data Valentina Boeva, Emmanuel Barillot, Institut Curie, valentina.boeva@curie.fr Jean-Francois Laes OncoDNA, jf.laes@oncodna.com The emergence of the amplicon sequencing technique, which followed whole exome sequencing, promises a revolution in cancer diagnostics and treatment. ... Visualization of the typical configuration of read mappings (with Integrative Genomics Viewer). ...

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