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

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 artificiall...

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Bibliographic Details
Published in:Genome Biology Vol. 25; no. 1; p. 60
Main Authors: 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., Brown, Larissa C., Clark, Karen, Davis, Emily W., Smith-White, Brian, Hlavina, Wratko, Pruitt, Kim D., Schneider, Valerie A., Murphy, Terence D.
Format: Journal Article
Language:English
Published: London BioMed Central 26.02.2024
Springer Nature B.V
BMC
Subjects:
Animal Genetics and Genomics
Archives & records
Automation
Bioinformatics
Biomedical and Life Sciences
Contaminants
Contamination
Databases, Nucleic Acid
Eukaryotes
Evolutionary Biology
Fungi
GenBank
Genome
Genome assembly
Genome contamination
Genome quality
Genomes
Genomics
Human Genetics
Life Sciences
Method
Microbial Genetics and Genomics
nucleotide sequences
Organisms
Plant Genetics and Genomics
Prokaryotes
rapid methods
RefSeq
screening
sequence analysis
Software
species
Taxonomy
RefSeq
Genome quality
Software
Genome assembly
Genome contamination
GenBank
ISSN:1474-760X, 1474-7596, 1474-760X
Online Access:Get full text
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Description
Summary: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 .
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-024-03198-7