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assembly.unplaced is an output file in RUN. It gives an accounting of unplaced reads in a draft assembly. It has a tab-delimited format; each row contains a read name, followed by a keyword indicating the reason why the read was not placed in the assembly. The values of that field can be:

     VALUE 	        MEANING
     deliberate 	excluded by configuration file reads_config.xml
     low_quality 	nothing left after quality-based trimming
     vector_or_host 	matches vector or bacterial host sequence
     mitochondrial 	matches mitochondrial sequence
     chimera 	        suspected of being chimeric
     unplaced 	        no problem with read, but not placed in contig
     other 	        some other reason

The higher the read usage, the smaller the file assembly.unplaced will be.

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