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

Autor(es)

Nayfach, Stephen ^[1] ; Camargo, Antonio Pedro ^[2] ; Schulz, Frederik ^[1] ; Eloe-Fadrosh, Emiley ^[1] ; Roux, Simon ^[1] ; Kyrpides, Nikos C. ^[1]

Afiliação do(s) autor(es)

^[1] US DOE, Joint Genome Inst, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 - USA

^[2] Univ Estadual Campinas, Inst Biol, Dept Genet Evolut Microbiol & Immunol, Campinas - Brazil

• Tipo de documento: Artigo Científico
• Fonte: NATURE BIOTECHNOLOGY; v. 39, n. 5 DEC 2020.
• Citações Web of Science: 8

Resumo

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. (AU)

• Processo FAPESP: 16/23218-0 - Centro de Pesquisa em Genômica Aplicada às Mudanças Climáticas
• Beneficiário: Edi Lúcia Sartorato
• Modalidade de apoio: Auxílio à Pesquisa - Programa Centros de Pesquisa em Engenharia
• Processo FAPESP: 18/04240-0 - Investigação metagenômica dos microbiomas de plantas adaptadas à limitação nutricional de fósforo
• Beneficiário: Antônio Pedro de Castello Branco da Rocha Camargo
• Modalidade de apoio: Bolsas no Brasil - Doutorado