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

被引：102

作者：

Astashyn, Alexander ^{[1
]}

Tvedte, Eric S. ^{[1
]}

Sweeney, Deacon ^{[1
]}

Sapojnikov, Victor ^{[1
]}

Bouk, Nathan ^{[1
]}

Joukov, Victor ^{[1
]}

Mozes, Eyal ^{[1
]}

Strope, Pooja K. ^{[1
]}

Sylla, Pape M. ^{[1
]}

Wagner, Lukas ^{[1
]}

Bidwell, Shelby L. ^{[1
]}

Brown, Larissa C. ^{[1
]}

Clark, Karen ^{[1
]}

Davis, Emily W. ^{[1
]}

Smith-White, Brian ^{[1
]}

Hlavina, Wratko ^{[1
]}

Pruitt, Kim D. ^{[1
]}

Schneider, Valerie A. ^{[1
]}

Murphy, Terence D. ^{[1
]}

机构：

[1] NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20892 USA

来源：

GENOME BIOLOGY | 2024年 / 25卷 / 01期

基金：

美国国家卫生研究院;

关键词：

Genome contamination; Genome quality; Genome assembly; GenBank; RefSeq; Software; GENE-TRANSFER;

D O I：

10.1186/s13059-024-03198-7

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：25