2022
DOI: 10.1186/s12859-022-04973-8
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VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

Abstract: Background With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving biodiversity is paramount not only for the Earth’s natural systems but also for discovering solutions to challenges that we face as a growing civilization. Metagenomics pertains to the in silico study of all microorganisms within an ecological community in situ, however, many s… Show more

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Cited by 13 publications
(19 citation statements)
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“…For metagenomic and metatranscriptomic data, we used the VEBA v1.0.3 suite of tools ( 95 ) for its robust ability to use ab initio , non-database-reliant methods for binning eukaryotic genomes. All modules were used in default settings unless stated here.…”
Section: Methodsmentioning
confidence: 99%
“…For metagenomic and metatranscriptomic data, we used the VEBA v1.0.3 suite of tools ( 95 ) for its robust ability to use ab initio , non-database-reliant methods for binning eukaryotic genomes. All modules were used in default settings unless stated here.…”
Section: Methodsmentioning
confidence: 99%
“…S1 and Table S1 , respectively. Metagenomic and metatranscriptomic workflows were performed using early versions of the VEBA software suite ( 51 ).…”
Section: Methodsmentioning
confidence: 99%
“…The classification protocol has been previously described (4) and the only modification is that it can now handle taxa with incomplete lineages such is the case for many protists and fungi. If genome clusters are provided, then it performs consensus lineage classification.…”
Section: Classify-eukaryotic -Taxonomic Classification Of Eukaryotic ...mentioning
confidence: 99%
“…However, aside from prophages, many microbiome studies focus primarily on the prokaryome (i.e., bacteria and archaea) and do not assess the eukaryome and virome from a genome-resolved perspective. The motivating factor for developing the Viral Eukaryotic Bacterial Archaeal ( VEBA ) open-source software suite (4) was to extend modular end-to-end (meta-)genomics/transcriptomics methodologies beyond the prokaryome to support the eukaryome and virome. The eukaryome in this context is defined as the fraction of microbes composed of nucleated organisms such as protists and unicellular fungi (adapted from (5)) while the virome consists of all the viruses within an ecosystem, including those integrated into host genomes (6).…”
Section: Introductionmentioning
confidence: 99%