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FCS

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

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

FCS-GX

FCS-GX detects contamination from foreign organisms in genome sequences using the GX (Genome Cross-species) aligner. 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. 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.

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