Viral Annotation Pipeline in KBase

Bolduc, Benjamin; Wood-Charlson, Elisha; Dehal, Paramvir; Crockett, Zachary

doi:10.25982/59912.37/1635154

Title: Viral Annotation Pipeline in KBase

Abstract

This data analysis workflow demonstrates how to process a metagenome to identify viruses using VirSorter. Then, provides taxonomic classification using vConTACT2.

Authors:

^[1];

^[2];

^[3]

The Ohio State Univ., Columbus, OH (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Publication Date:: 2020-06-28

Research Org.:: Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); The Ohio State Univ., Columbus, OH (United States); U.S. Department of Energy Systems Biology Knowledgebase; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1635154

DOE Contract Number:: AC02-05CH11231, AC02-06CH11357, AC05-00OR22725,

Resource Type:: Data

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Virus; Genomics; Bioinformatics

Citation Formats


                    Bolduc, Benjamin, Wood-Charlson, Elisha, Dehal, Paramvir, and Crockett, Zachary. Viral Annotation Pipeline in KBase.  United States: N. p., 2020. 
        Web.  doi:10.25982/59912.37/1635154.

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                    Bolduc, Benjamin, Wood-Charlson, Elisha, Dehal, Paramvir, & Crockett, Zachary. Viral Annotation Pipeline in KBase.  United States.  https://doi.org/10.25982/59912.37/1635154

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                    Bolduc, Benjamin, Wood-Charlson, Elisha, Dehal, Paramvir, and Crockett, Zachary. 2020.  
        "Viral Annotation Pipeline in KBase".  United States.  https://doi.org/10.25982/59912.37/1635154.  https://www.osti.gov/servlets/purl/1635154.

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@article{osti_1635154,

  title        = {Viral Annotation Pipeline in KBase},

  author       = {Bolduc, Benjamin and Wood-Charlson, Elisha and Dehal, Paramvir and Crockett, Zachary},

  abstractNote = {This data analysis workflow demonstrates how to process a metagenome to identify viruses using VirSorter. Then, provides taxonomic classification using vConTACT2.},

  doi          = {10.25982/59912.37/1635154},

  url          = {https://www.osti.gov/biblio/1635154},
  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2020},

  month        = {6}

}

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Dataset:

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https://doi.org/10.25982/59912.37/1635154

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Works referenced in this record:

Prokka: rapid prokaryotic genome annotation
journal, March 2014

Seemann, T.
Bioinformatics, Vol. 30, Issue 14
https://doi.org/10.1093/bioinformatics/btu153

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
journal, May 2019

Bin Jang, Ho; Bolduc, Benjamin; Zablocki, Olivier
Nature Biotechnology, Vol. 37, Issue 6
https://doi.org/10.1038/s41587-019-0100-8

VirSorter: mining viral signal from microbial genomic data
journal, January 2015

Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.
PeerJ, Vol. 3
https://doi.org/10.7717/peerj.985

KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018

Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.
Nature Biotechnology, Vol. 36, Issue 7
https://doi.org/10.1038/nbt.4163

VirSorter: mining viral signal from microbial genomic data
journal, January 2015

Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.
PeerJ, Vol. 3
https://doi.org/10.7717/peerj.985

Works referencing / citing this record:

KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018

Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.
Nature Biotechnology, Vol. 36, Issue 7
https://doi.org/10.1038/nbt.4163

VirSorter: mining viral signal from microbial genomic data
journal, January 2015

Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.
PeerJ, Vol. 3
https://doi.org/10.7717/peerj.985

Prokka: rapid prokaryotic genome annotation
journal, March 2014

Seemann, T.
Bioinformatics, Vol. 30, Issue 14
https://doi.org/10.1093/bioinformatics/btu153

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
journal, May 2019

Bin Jang, Ho; Bolduc, Benjamin; Zablocki, Olivier
Nature Biotechnology, Vol. 37, Issue 6
https://doi.org/10.1038/s41587-019-0100-8

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Similar Records

Title: Viral Annotation Pipeline in KBase

Abstract

Citation Formats

Prokka: rapid prokaryotic genome annotation journal, March 2014

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks journal, May 2019

VirSorter: mining viral signal from microbial genomic data journal, January 2015

KBase: The United States Department of Energy Systems Biology Knowledgebase journal, July 2018

VirSorter: mining viral signal from microbial genomic data journal, January 2015

KBase: The United States Department of Energy Systems Biology Knowledgebase journal, July 2018

VirSorter: mining viral signal from microbial genomic data journal, January 2015

Prokka: rapid prokaryotic genome annotation journal, March 2014

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks journal, May 2019

Prokka: rapid prokaryotic genome annotation
journal, March 2014

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
journal, May 2019

VirSorter: mining viral signal from microbial genomic data
journal, January 2015

KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018

VirSorter: mining viral signal from microbial genomic data
journal, January 2015

KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018

VirSorter: mining viral signal from microbial genomic data
journal, January 2015

Prokka: rapid prokaryotic genome annotation
journal, March 2014

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
journal, May 2019