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.