Rapid and sensitive detection of genome contamination at scale with FCS-GX.
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2024
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Abstract
Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI's Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. FCS-GX screens most genomes in 0.1-10 min. Testing FCS-GX on artificially fragmented genomes demonstrates high sensitivity and specificity for diverse contaminant species. We used FCS-GX to screen 1.6 million GenBank assemblies and identified 36.8 Gbp of contamination, comprising 0.16% of total bases, with half from 161 assemblies. We updated assemblies in NCBI RefSeq to reduce detected contamination to 0.01% of bases. FCS-GX is available at https://github.com/ncbi/fcs/ or https://doi.org/10.5281/zenodo.10651084 .
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astashyn2024rapidgenome
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| Authors | Astashyn, Alexander;Tvedte, Eric S;Sweeney, Deacon;Sapojnikov, Victor;Bouk, Nathan;Joukov, Victor;Mozes, Eyal;Strope, Pooja K;Sylla, Pape M;Wagner, Lukas;Bidwell, Shelby L;Brown, Larissa C;Clark, Karen;Davis, Emily W;Smith-White, Brian;Hlavina, Wratko;Pruitt, Kim D;Schneider, Valerie A;Murphy, Terence D; |
| Journal | Genome biology |
| Year | 2024 |
| DOI |
60
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| URL | |
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