The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). FCS-GX aligns sequences to a large database of NCBI genomes through modified k-mer seeds and assign a most likely taxonomic division. FCS-GX classifies sequences as contaminant when their taxonomic assignment is different from the user provided taxonomic identifier. A contamination summary provides an overview of observed contaminant divisions, counts, and total sizes, and an action report provides details and recommended actions for each problematic sequence.