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

Clicks: 203
ID: 278319
2024
Article Quality & Performance Metrics
Overall Quality
Not rated
Combines reader engagement with the AI quality analysis. This article has not been analysed, so there is no overall score — reader engagement is measured and shown alongside.
AI Quality Assessment
Not analyzed
Readership in this journal
Emerging

Ranked #15 of 24 articles by views in Genome biology

Most read Least read

Bar heights use a square-root scale.

Mint this article as an NFT
Not yet minted

Create a permanent, verifiable on-chain record of this article on the Scimatic Network. The NFT is held in your Journament account, and you can withdraw it to your own wallet at any time.

5 SUSD one-off · no wallet required
Sign in to mint
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 .
Reference Key
astashyn2024rapidgenome Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
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;
Journal Genome biology
Year 2024
DOI
60
URL
Keywords
software genome assembly genbank genome contamination genome quality refseq

Citations

No citations found. To add a citation, contact the admin at info@scimatic.org

Comments

No comments yet. Be the first to comment on this article.