학술논문
Rapid and sensitive detection of genome contamination at scale with FCS-GX
Document Type
article
Author
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; Larissa C. Brown; Karen Clark; Emily W. Davis; Brian Smith-White; Wratko Hlavina; Kim D. Pruitt; Valerie A. Schneider; Terence D. Murphy
Source
Genome Biology, Vol 25, Iss 1, Pp 1-25 (2024)
Subject
Language
English
ISSN
1474-760X
Abstract
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 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 .