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

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

doi:10.1101/2023.06.02.543519

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

bioRxiv [Preprint]. 2023 Jun 6:2023.06.02.543519. doi: 10.1101/2023.06.02.543519.

Authors

Alexander Astashyn¹, Eric S Tvedte¹, Deacon Sweeney¹, Victor Sapojnikov¹, Nathan Bouk¹, Victor Joukov¹, Eyal Mozes¹, Pooja K Strope¹, Pape M Sylla¹, Lukas Wagner¹, Shelby L Bidwell¹, Karen Clark¹, Emily W Davis¹, Brian Smith-White¹, Wratko Hlavina¹, Kim D Pruitt¹, Valerie A Schneider¹, Terence D Murphy¹

Affiliation

¹ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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 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/.

Keywords: GenBank; Genome assembly; Genome contamination; Genome quality; RefSeq; Software.

Publication types

Preprint

Grants and funding

WT_/Wellcome Trust/United Kingdom