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

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

in Bioinformatics

2023

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

in Bioinformatics

2023

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Journal Article

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

Wagner, Lukas,

Clark, Karen,

Mozes, Eyal,

Bidwell, Shelby L,

Sylla, Pape M,

Davis, Emily W,

Sweeney, Deacon,

Bouk, Nathan,

Tvedte, Eric S,

Murphy, Terence D,

Astashyn, Alexander,

Hlavina, Wratko,

Joukov, Victor,

Smith-White, Brian,

Pruitt, Kim D,

Strope, Pooja K,

Schneider, Valerie A,

Sapojnikov, Victor

2023

Overview

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 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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Publisher

Cold Spring Harbor Laboratory

Subject

Bioinformatics