Login / Signup

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

Alexander AstashynEric S TvedteDeacon SweeneyVictor SapojnikovNathan BoukVictor JoukovEyal MozesPooja K StropePape M SyllaLukas WagnerShelby L BidwellLarissa C BrownKaren ClarkEmily W DavisBrian Smith-WhiteWratko HlavinaKim D PruittValerie A SchneiderTerence D Murphy
Published in: Genome biology (2024)
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 .
Keyphrases
  • sensitive detection
  • risk assessment
  • drinking water
  • health risk
  • high throughput
  • human health
  • genome wide
  • quantum dots
  • loop mediated isothermal amplification
  • climate change