KBase Narrative - Viral Analysis End-to-End

Name: KBase Narrative - Viral Analysis End-to-End
Published: Thu May 12 04:00:00 EDT 2022

Bolduc, Benjamin

doi:10.25982/75811.86/1868934

KBase Narrative - Viral Analysis End-to-End

Dataset · Thu May 12 04:00:00 EDT 2022

DOI:https://doi.org/10.25982/75811.86/1868934· OSTI ID:1868934

^[1]

The Ohio State University; Lawrence Berkeley National Laboratory (LBNL)

This pipeline processes a single metagenomic dataset (downloaded from NCBI SRA) from the Global Ocean Viromes dataset, identifies the viral sequences using VirSorter, and subsequently classifies them with vConTACT2. Along the way there are several intermediary steps to convert files from one KBase object to another - and though some of these can be skipped for this particular dataset - we're explicitly doing them here as to be more easily generalized to other datasets.

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Research Organization:: U.S. Department of Energy Systems Biology Knowledgebase

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

OSTI ID:: 1868934

Country of Publication:: United States

Language:: English

References (25)

VirSorter: mining viral signal from microbial genomic data Roux, Simon; Enault, Francois; Hurwitz, Bonnie L. PeerJ, Vol. 3 https://doi.org/10.7717/peerj.985	journal	January 2015
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses Roux, Simon; Brum, Jennifer R.; Dutilh, Bas E. Nature, Vol. 537, Issue 7622 https://doi.org/10.1038/nature19366	journal	September 2016
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3243	journal	January 2017
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity Roux, Simon; Emerson, Joanne B.; Eloe-Fadrosh, Emiley A. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3817	journal	January 2017
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
The viable but nonculturable phenotype: a crossroads in the life-cycle of non-differentiating bacteria? Barcina, Isabel; Arana, Inés Reviews in Environmental Science and Bio/Technology, Vol. 8, Issue 3 https://doi.org/10.1007/s11157-009-9159-x	journal	April 2009
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
Status of the Microbial Census Schloss, P. D.; Handelsman, J. Microbiology and Molecular Biology Reviews, Vol. 68, Issue 4 https://doi.org/10.1128/MMBR.68.4.686-691.2004	journal	December 2004
The virophage as a unique parasite of the giant mimivirus La Scola, Bernard; Desnues, Christelle; Pagnier, Isabelle Nature, Vol. 455, Issue 7209 https://doi.org/10.1038/nature07218	journal	August 2008
Prophages and bacterial genomics: what have we learned so far?: Prophage genomics Casjens, Sherwood Molecular Microbiology, Vol. 49, Issue 2 https://doi.org/10.1046/j.1365-2958.2003.03580.x	journal	June 2003
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks Bin Jang, Ho; Bolduc, Benjamin; Zablocki, Olivier Nature Biotechnology, Vol. 37, Issue 6 https://doi.org/10.1038/s41587-019-0100-8	journal	May 2019
Using SPAdes De Novo Assembler Prjibelski, Andrey; Antipov, Dmitry; Meleshko, Dmitry Current Protocols in Bioinformatics, Vol. 70, Issue 1 https://doi.org/10.1002/cpbi.102	journal	June 2020
Prokka: rapid prokaryotic genome annotation Seemann, T. Bioinformatics, Vol. 30, Issue 14 https://doi.org/10.1093/bioinformatics/btu153	journal	March 2014
Initial sequencing and analysis of the human genome Lander, Eric S.; Linton, Lauren M. Nature, Vol. 409, Issue 6822, p. 860-921 https://doi.org/10.1038/35057062	journal	February 2001
Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts Sullivan, Matthew B.; Lindell, Debbie; Lee, Jessica A. PLoS Biology, Vol. 4, Issue 8 https://doi.org/10.1371/journal.pbio.0040234	journal	July 2006
Movement of Viruses between Biomes Sano, E.; Carlson, S.; Wegley, L. Applied and Environmental Microbiology, Vol. 70, Issue 10 https://doi.org/10.1128/AEM.70.10.5842-5846.2004	journal	October 2004
Here a virus, there a virus, everywhere the same virus? Breitbart, Mya; Rohwer, Forest Trends in Microbiology, Vol. 13, Issue 6 https://doi.org/10.1016/j.tim.2005.04.003	journal	June 2005
metaSPAdes: a new versatile metagenomic assembler Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.213959.116	journal	March 2017
Marine viruses — major players in the global ecosystem Suttle, Curtis A. Nature Reviews Microbiology, Vol. 5, Issue 10 https://doi.org/10.1038/nrmicro1750	journal	October 2007
Sulfur Oxidation Genes in Diverse Deep-Sea Viruses Anantharaman, K.; Duhaime, M. B.; Breier, J. A. Science, Vol. 344, Issue 6185 https://doi.org/10.1126/science.1252229	journal	May 2014
Marine viruses and their biogeochemical and ecological effects Fuhrman, Jed A. Nature, Vol. 399, Issue 6736 https://doi.org/10.1038/21119	journal	June 1999
Viruses in the sea Suttle, Curtis A. Nature, Vol. 437, Issue 7057 https://doi.org/10.1038/nature04160	journal	September 2005
Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics Roux, Simon; Hawley, Alyse K.; Torres Beltran, Monica eLife, Vol. 3 https://doi.org/10.7554/eLife.03125	journal	August 2014
Human Endogenous Retroviruses Are Ancient Acquired Elements Still Shaping Innate Immune Responses Grandi, Nicole; Tramontano, Enzo Frontiers in Immunology, Vol. 9 https://doi.org/10.3389/fimmu.2018.02039	journal	September 2018
Prophage Genomics Canchaya, C.; Proux, C.; Fournous, G. Microbiology and Molecular Biology Reviews, Vol. 67, Issue 2 https://doi.org/10.1128/MMBR.67.2.238-276.2003	journal	June 2003

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