CheckV assesses the quality and completeness of metagenome-assembled viral genomes

By Stephen Nayfach, Antonio Pedro Camargo, Frederik Schulz, Emily Eloe-Fadrosh, Simon Roux, Nikos Kyrpides. Nature Biotechnology, 2020

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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. The quality of viral genomes assembled from metagenome data is assessed by CheckV.

Subfields: Ecology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/21818286078368e92b4a84194872737ee45732ef

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Citations in the corpus

IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses (2020, methodology): “(D) Fraction of high-quality genomes (≥90% estimated completeness), and genome fragments of ≥50% and < 50% estimated completeness, as based on CheckV (27), in IMG/VR v3.”
Petabase-scale sequence alignment catalyses viral discovery (2020, methodology): “The first method is CheckV [95], followed selecting contigs associated to known CoV genomes.”
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes (2021, background): “Complementing technical measures like the N50 value, biologically meaningful metrics based on expected gene content have proved to be useful for estimating the quality of genomes, as exemplified by our BUSCO tool (Sim~ao et al. 2015; Waterhouse et al. 2018), the now discontinued CEGMA (Parra et al. ”
Identification of mobile genetic elements with geNomad (2023, neutral): “To reduce sequence redundancy, plasmid and virus scaffolds were de-replicated using pairwise average nucleotide identities (ANIs), computed as described in Nayfach et al. 40 (code available at https://bitbucket.org/berkeleylab/checkv/src/master/scripts/anicalc.py).”