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-adaptor detects adaptor and vector contamination in genome sequences. FCS-adaptor is a high-throughput implementation of NCBI VecScreen. The FCS-adaptor executable retrieves a Docker or Singularity container and runs a pipeline to screen input sequences against a database of adaptors and vectors using stringent BLAST searches.

Please read the wiki for instructions on how to run FCS-adaptor.

FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). The FCS-GX executable retrieves a Docker or Singularity container and runs a pipeline to align 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.

Please read the wiki for instructions on how to run FCS-GX.

❗ FCS is live on on Galaxy! Tutorial here.

Astashyn A, Tvedte ES, Sweeney D, Sapojnikov V, Bouk N, Joukov V, Mozes E, Strope PK, Sylla PM, Wagner L, Bidwell SL, Brown LC, Clark K, Davis EW, Smith-White B, Hlavina W, Pruitt KD, Schneider VA, Murphy TD. Rapid and sensitive detection of genome contamination at scale with FCS-GX. Genome Biol. 2024 Feb 26;25(1):60. doi: 10.1186/s13059-024-03198-7. PMID: 38409096; PMCID: PMC10898089.

Read the FCS-GX paper

The NCBI FCS tool suite software authored by NCBI is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties as United States Government employees and thus cannot be copyrighted. This software is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction.

Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose.

Please cite NCBI in any work or product based on this material.

This work was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM), National Institutes of Health.

FCS is part of the NIH Comparative Genomics Resource (CGR), an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms.