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bioRxiv · 10.1101/2023.06.02.543519

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

Astashyn, A.·Tvedte, E. S.·Sweeney, D.·Sapojnikov, V.·Bouk, N.·Joukov, V.·Mozes, E.·Strope, P. K.·Sylla, P. M.·Wagner, L.·Bidwell, S. L.·Clark, K.·Davis, E. W.·Smith-White, B.·Hlavina, W.·Pruitt, K. D.·Schneider, V. A.·Murphy, T. D.
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Abstract

Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBIs 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 minutes. Testing FCS-GX on artificially fragmented genomes demonstrates sensitivity >95% for diverse contaminant species and specificity >99.93%. We used FCS-GX to screen 1.6 million GenBank assemblies and identified 36.8 Gbp of contamination (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/.

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Astashyn, A., Tvedte, E. S., Sweeney, D., Sapojnikov, V., Bouk, N., Joukov, V., Mozes, E., Strope, P. K., Sylla, P. M., Wagner, L., Bidwell, S. L., Clark, K., Davis, E. W., Smith-White, B., Hlavina, W., Pruitt, K. D., Schneider, V. A., Murphy, T. D.. 2023-06-06. Rapid and sensitive detection of genome contamination at scale with FCS-GX. https://doi.org/10.1101/2023.06.02.543519

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