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Rapid and sensitive detection of genome contamination at scale with FCS-GX

2024; BioMed Central; Volume: 25; Issue: 1 Linguagem: Inglês

10.1186/s13059-024-03198-7

1474-760X

Alexander Astashyn, Eric S. Tvedte, Deacon Sweeney, Victor Sapojnikov, Nathan Bouk, Victor Joukov, Eyal Mozes, Pooja K Strope, Pape M. Sylla, Lukas Wagner, Shelby Bidwell, Larissa C. Brown, Karen Clark, Emily W. Davis, Brian Smith-White, Wratko Hlavina, Kim D. Pruitt, Valérie Schneider, Terence D. Murphy,

Molecular Biology Techniques and Applications

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 .