The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.
Rapid and sensitive detection of genome contamination at scale with FCS-GX
Open accessAbstract
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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“The FCS-GX classification system uses eight larger taxonomic “kingdoms”: animals (Metazoa), plants (Viridiplantae), Fungi, protists (other Eukaryota), Bacteria, Archaea, Viruses, and Synthetic [21, 22].”
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Cited by
NCBI RefSeq: reference sequence standards through 25 years of curation and annotation
Goldfarb, T., Kodali, V. K., Pujar, S., Brover, V., Robbertse, B., Farrell, C. M., Oh, D.-H., Astashyn, A., Ermolaeva, O., Haddad, D., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1038 · Cited by 455
Self-citationParallel gene expansions drive rapid dietary adaptation in herbivorous woodrats
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Molecular mechanisms of plastic biodegradation by the fungus Clonostachys rosea
Gambarini, V., Pavlov, N., Young, P., Dawes, S., Auffret, A., Kingsbury, J. M., Donaldson, L. A., Smith, D. A., Weaver, L., Pantos, O., et al. (2025) · mBio · doi:10.1128/mbio.00335-25 · Cited by 10
Metadata
- Authors
- Astashyn, A., Tvedte, E. S., Sweeney, D., Sapojnikov, V., Bouk, N., Joukov, V., Mozes, E., Strope, P. K., Sylla, P. M., Wagner, L., Bidwell, S. L., Brown, L. C., Clark, K., Davis, E. W., Smith-White, B., Hlavina, W., Pruitt, K. D., Schneider, V. A., & Murphy, T. D.
- Venue
- Genome Biology
- Published
- 2024-02-26
- Volume
- 25
- Issue
- 1
- Pages
- 60-60
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W4392155646
- Cited by
- 469
- References
- 36
- FWCI
- 54.03
- Type
- journal article
- Language
- en
- Open access
- gold
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- Astashyn, A., Tvedte, E. S., Sweeney, D., Sapojnikov, V., Bouk, N., Joukov, V., Mozes, E., Strope, P. K., Sylla, P. M., Wagner, L., Bidwell, S. L., Brown, L. C., Clark, K., Davis, E. W., Smith-White, B., Hlavina, W., Pruitt, K. D., Schneider, V. A., & Murphy, T. D. (2024). Rapid and sensitive detection of genome contamination at scale with FCS-GX. Genome Biology. https://doi.org/10.1186/s13059-024-03198-7
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