Evidence map›Paper›PMID 37292984›Full record

ArticlebioRxiv : the preprint server for biology2023

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

Alexander Astashyn, Eric S Tvedte, Deacon Sweeney, Victor Sapojnikov, Nathan Bouk, Victor Joukov, Eyal Mozes, Pooja K Strope, Pape M Sylla, Lukas Wagner and 8 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors.

Alexander AstashynNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Eric S TvedteNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Deacon SweeneyNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Victor SapojnikovNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Nathan BoukNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Victor JoukovNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Eyal MozesNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Pooja K StropeNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Pape M SyllaNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Lukas WagnerNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Shelby L BidwellNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Karen ClarkNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Emily W DavisNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Brian Smith-WhiteNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Wratko HlavinaNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Kim D PruittNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Valerie A SchneiderNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Terence D MurphyNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

Funding

Wellcome Trust
6 · The paper itself

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/.

Indexed as

GenBankGenome assemblyGenome contaminationGenome qualityRefSeqSoftware

Identifiers

PMID37292984
PMCPMC10246020

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.