CheckV assesses the quality and completeness of metagenome-assembled viral genomes
Lawrence Berkeley National Laboratory · Joint Genome Institute · +1 more institution
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…
Citation impact
- FWCI
- 97.76
- Percentile
- 100%
- References
- 83
Authors
6- SNStephen NayfachCorresponding
Lawrence Berkeley National Laboratory, Joint Genome Institute
- APAntônio Pedro Camargo
Universidade Estadual de Campinas (UNICAMP)
- FSFrederik Schulz
Lawrence Berkeley National Laboratory, Joint Genome Institute
- EAEmiley A. Eloe‐Fadrosh
Lawrence Berkeley National Laboratory, Joint Genome Institute
- SRSimon Roux
Lawrence Berkeley National Laboratory, Joint Genome Institute
Topics & keywords
- Genome
- Human virome
- Metagenomics
- Biology
- Computational biology
- Completeness (order theory)
- Genetics
- Gene
- Life below water
Funding
- UDU.S. Department of EnergyAwards: -AC02-05CH11231, 05CH11231, AC02-05CH11231, DE-AC02, DE-AC02-05CH11231, DE-AC02-
- JGJoint Genome InstituteAwards: DE-AC02-05CH11231, AC02-05CH11231
- FDFundação de Amparo à Pesquisa do Estado de São PauloAwards: 2016/23218-0, 2018/04240-0
- OOOffice of ScienceAwards: AC02-05CH11231, -AC02-05CH11231, DE-AC02
- PDPro-Reitoria de Pesquisa, Universidade de São PauloAward: 2016/23218-0