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Rapid and sensitive detection of genome contamination at scale with FCS-GX.
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; Clark, Karen; Davis, Emily W; Smith-White, Brian; Hlavina, Wratko; Pruitt, Kim D; Schneider, Valerie A; Murphy, Terence D.
Afiliação
  • Astashyn A; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Tvedte ES; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Sweeney D; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Sapojnikov V; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Bouk N; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Joukov V; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Mozes E; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Strope PK; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Sylla PM; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Wagner L; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Bidwell SL; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Clark K; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Davis EW; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Smith-White B; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Hlavina W; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Pruitt KD; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Schneider VA; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • Murphy TD; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
bioRxiv ; 2023 06 06.
Article em En | MEDLINE | ID: mdl-37292984
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/.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Tipo de estudo: Diagnostic_studies Idioma: En Revista: BioRxiv Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Tipo de estudo: Diagnostic_studies Idioma: En Revista: BioRxiv Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos