Minimum information about an uncultivated virus genome (MIUVIG)
Simon Roux,Evelien M. Adriaenssens,Bas E. Dutilh,Eugene V. Koonin,Andrew M. Kropinski,Mart Krupovic,Jens H. Kuhn,Rob Lavigne,J. Rodney Brister,Arvind Varsani,Arvind Varsani,Clara Amid,Ramy K. Aziz,Seth R. Bordenstein,Peer Bork,Mya Breitbart,Guy Cochrane,Rebecca A. Daly,Christelle Desnues,Melissa B. Duhaime,Joanne B. Emerson,François Enault,Jed A. Fuhrman,Pascal Hingamp,Philip Hugenholtz,Bonnie L. Hurwitz,Natalia Ivanova,Jessica M. Labonté,Kyung Bum Lee,Rex R. Malmstrom,Manuel Martinez-Garcia,Ilene Karsch Mizrachi,Hiroyuki Ogata,David Paez-Espino,Marie-Agnès Petit,Catherine Putonti,Thomas Rattei,Alejandro Reyes,Francisco Rodriguez-Valera,Karyna Rosario,Lynn M. Schriml,Frederik Schulz,Grieg F. Steward,Matthew B. Sullivan,Shinichi Sunagawa,Curtis A. Suttle,Ben Temperton,Susannah G. Tringe,Rebecca Vega Thurber,Nicole S. Webster,Nicole S. Webster,Katrine Whiteson,Steven W. Wilhelm,K. Eric Wommack,Tanja Woyke,Kelly C. Wrighton,Pelin Yilmaz,Takashi Yoshida,Mark J. Young,Natalya Yutin,Lisa Zeigler Allen,Lisa Zeigler Allen,Nikos C. Kyrpides,Emiley A. Eloe-Fadrosh +63 more
TLDR
The MIUViG (Minimum Information about an Uncultivated Virus Genome) as mentioned in this paper standard was developed within the Genomic Standards Consortium framework and includes virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction.Abstract:
We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.read more
Citations
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Marine DNA Viral Macro- and Microdiversity from Pole to Pole.
Ann C. Gregory,Ahmed A. Zayed,Nádia Conceição-Neto,Ben Temperton,Ben Bolduc,Adriana Alberti,Mathieu Ardyna,Ksenia Arkhipova,Margaux Carmichael,Corinne Cruaud,Céline Dimier,Céline Dimier,Guillermo Dominguez-Huerta,Joannie Ferland,Stefanie Kandels,Yunxiao Liu,Claudie Marec,Stephane Pesant,Marc Picheral,Sergey Pisarev,Julie Poulain,Jean-Éric Tremblay,Dean R. Vik,Silvia G. Acinas,Marcel Babin,Peer Bork,Emmanuel Boss,Chris Bowler,Guy Cochrane,Colomban de Vargas,Michael J. Follows,Gabriel Gorsky,Nigel Grimsley,Lionel Guidi,Pascal Hingamp,Daniele Iudicone,Olivier Jaillon,Stefanie Kandels-Lewis,Lee Karp-Boss,Eric Karsenti,Fabrice Not,Hiroyuki Ogata,Nicole J. Poulton,Jeroen Raes,Christian Sardet,Sabrina Speich,Lars Stemmann,Matthew B. Sullivan,Shinichi Sunagawa,Patrick Wincker,Alexander I. Culley,Bas E. Dutilh,Bas E. Dutilh,Simon Roux +53 more
TL;DR: An ∼12-fold expanded global ocean DNA virome dataset is established of 195,728 viral populations, now including the Arctic Ocean, and it is validated that these populations form discrete genotypic clusters.
Journal ArticleDOI
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
Ho Bin Jang,Benjamin Bolduc,Olivier Zablocki,Jens H. Kuhn,Simon Roux,Evelien M. Adriaenssens,Evelien M. Adriaenssens,J. Rodney Brister,Andrew M. Kropinski,Andrew M. Kropinski,Mart Krupovic,Rob Lavigne,Dann Turner,Matthew B. Sullivan +13 more
TL;DR: This work presents vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions, and applies it to analyze 15,280 Global Ocean Virome genome fragments.
Journal ArticleDOI
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences.
TL;DR: VIBRANT is the first method to utilize a hybrid machine learning and protein similarity approach that is not reliant on sequence features for automated recovery and annotation of viruses, determination of genome quality and completeness, and characterization of viral community function from metagenomic assemblies.
Journal ArticleDOI
CheckV assesses the quality and completeness of metagenome-assembled viral genomes.
Stephen Nayfach,Antonio P. Camargo,Frederik Schulz,Emiley A. Eloe-Fadrosh,Simon Roux,Nikos C. Kyrpides +5 more
TL;DR: CheckV as discussed by the authors is an automated pipeline for identifying closed closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses, which significantly improves the accuracy of identification of auxiliary metabolic genes and interpretation of viral-encoded functions.
Journal ArticleDOI
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses.
Jiarong Guo,Ben Bolduc,Ahmed A. Zayed,Arvind Varsani,Arvind Varsani,Guillermo Dominguez-Huerta,Tom O. Delmont,Akbar Adjie Pratama,M. Consuelo Gazitúa,Dean R. Vik,Matthew B. Sullivan,Simon Roux +11 more
TL;DR: VirSorter2 as mentioned in this paper is a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection.
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