FCS-GX
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Description
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.
Files
README.md
Additional details
References
- 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. biorXiv. (2023).