FCS-adaptor is a high-throughput implementation of NCBI VecScreen. FCS-adaptor runs a pipeline to screen input sequences against a non-redudant database of adaptors and vectors using stringent BLAST searches and remove contaminants from your genome.
FCS-adaptor removes terminal and internal matches to foreign sequences. Sequences identified as mostly adaptor/vector are removed entirely. FCS-adaptor produces a tabular output with details on the contaminant sequences identified as well as a cleaned FASTA.
Please see the wiki for more information.