ArticleNature biotechnology2021
CheckV assesses the quality and completeness of metagenome-assembled viral genomes.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,150 papers, 1 of them a synthesis that pooled it.
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Who cites it
1,150 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Cervicovaginal Virome Restructuring Associated with HPV Status, Bacterial Dysbiosis, and Cervical Cytological Abnormalities.Viruses · 2026Article
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- Phage Genomics and Bioinformatics in Therapeutic Development: Evidence Limits, Validation Gates, and Translational Decision-Making.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Viral Metagenomic Analysis of Bat Fly Pupae.Pathogens (Basel, Switzerland) · 2026Article
- Three thousand five hundred years of sheeppox virus evolution inferred from archaeological and codicological genomes.Science advances · 2026Article
- Genomic characterization and therapeutic potential of five broad-spectrum lytic bacteriophages against multidrug-resistant avian pathogenicMicrobiology spectrum · 2026Article
1,090 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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