The DOI matches its Crossref record; 68 of the 68 references it cites were found in a registry or an index.
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
Open accessAbstract
Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077
KEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
Prokka: rapid prokaryotic genome annotation
Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,818
Fast and sensitive protein alignment using DIAMOND
Buchfink, B., Xie, C., & Huson, D. H. (2015) · Nature Methods · doi:10.1038/nmeth.3176 · Cited by 14,201
The Pfam Protein Families Database
Bateman, A. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.276 · Cited by 14,000
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Capella-Gutiérrez, S., Silla-Martínez, J. M., & Gabaldón, T. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp348 · Cited by 12,751
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496
Research works printed but not linked: 3
- Smits, S. L. et al. Assembly of viral genomes from metagenomes. Front. Microbiol. 5, 714 (2014). · doi:10.3389/fmicb.2014.00714
- Chung, C. H. et al. Predicting genome terminus sequences of Bacillus cereus–group bacteriophage using next generation sequencing data. BMC Genomics 18, 350 (2017).
- Savilahti, H. & Bamford, D. H. Linear DNA replication: inverted terminal repeats of five closely related Escherichia coli bacteriophages. Gene 49, 199–205 (1986). · doi:10.1016/0378-1119(86)90280-5
Cited by
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab199 · Cited by 6,187
Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01688-w · Cited by 1,442
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
Nayfach, S., Páez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., Proal, A. D., Fischbach, M. A., Bhatt, A. S., Hugenholtz, P., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00928-6 · Cited by 580
Self-citationMassive expansion of human gut bacteriophage diversity
Camarillo-Guerrero, L. F., Almeida, A., Rangel-Pineros, G., Finn, R. D., & Lawley, T. D. (2021) · Cell · doi:10.1016/j.cell.2021.01.029 · Cited by 594
Camargo, A. P., Nayfach, S., Chen, I.-M. A., Palaniappan, K., Ratner, A., Chu, K., Ritter, S. J., Reddy, T. B. K., Mukherjee, S., Schulz, F., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1037 · Cited by 446
Self-citation
Metadata
- Authors
- Nayfach, S., Camargo, A. P., Schulz, F., Eloe-Fadrosh, E., Roux, S., & Kyrpides, N. C.
- Venue
- Nature Biotechnology
- Published
- 2020-12-21
- Volume
- 39
- Issue
- 5
- Pages
- 578-585
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W3118048495
- Cited by
- 1,750
- References
- 68
- FWCI
- 66.62
- Type
- journal article
- Language
- en
- Open access
- hybrid
- Licence
- creativecommons.org/licenses/by/4.0 (tdm)
- creativecommons.org/licenses/by/4.0 (vor)
- Funders
- U.S. Department of Energy (DE-AC02-05CH11231)
- University of São Paulo | Pro-Reitoria de Pesquisa, Universidade de São Paulo (2016/23218-0)
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: CheckV assesses the quality and completeness of metagenome-assembled viral genomes. https://app.cochat.ai/papers/10.1038/s41587-020-00774-7
- The paper
- Nayfach, S., Camargo, A. P., Schulz, F., Eloe-Fadrosh, E., Roux, S., & Kyrpides, N. C. (2021). CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nature Biotechnology. https://doi.org/10.1038/s41587-020-00774-7
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
