Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
Abstract
Background: Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we usedin silicomock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. Results: Tools specifically designed for metagenomes, specifically metaSPAdes, MEGAHIT, and IDBA-UD, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5 × coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥97%) and when the most abundant strain represented <50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥10 kb contig lengths to definemore »
- Authors:
-
- The Ohio State Univ., Columbus, OH (United States). Department of Microbiology
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- The Ohio State Univ., Columbus, OH (United States). Department of Microbiology and Department of Civil, Environmental and Geodetic Engineering
- Publication Date:
- Research Org.:
- Univ. of Arizona, Tucson, AZ (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1424953
- Alternate Identifier(s):
- OSTI ID: 1581051
- Grant/Contract Number:
- SC0010580; SC0016440; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PeerJ
- Additional Journal Information:
- Journal Volume: 5; Journal ID: ISSN 2167-8359
- Publisher:
- PeerJ Inc.
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Bioinformatics; Ecology; Genomics; Microbiology
Citation Formats
Roux, Simon, Emerson, Joanne B., Eloe-Fadrosh, Emiley A., and Sullivan, Matthew B. Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. United States: N. p., 2017.
Web. doi:10.7717/peerj.3817.
Roux, Simon, Emerson, Joanne B., Eloe-Fadrosh, Emiley A., & Sullivan, Matthew B. Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. United States. https://doi.org/10.7717/peerj.3817
Roux, Simon, Emerson, Joanne B., Eloe-Fadrosh, Emiley A., and Sullivan, Matthew B. Thu .
"Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity". United States. https://doi.org/10.7717/peerj.3817. https://www.osti.gov/servlets/purl/1424953.
@article{osti_1424953,
title = {Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity},
author = {Roux, Simon and Emerson, Joanne B. and Eloe-Fadrosh, Emiley A. and Sullivan, Matthew B.},
abstractNote = {Background: Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we usedin silicomock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. Results: Tools specifically designed for metagenomes, specifically metaSPAdes, MEGAHIT, and IDBA-UD, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5 × coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥97%) and when the most abundant strain represented <50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥10 kb contig lengths to define populations, (ii) coverage defined from reads mapping at ≥90% identity, and (iii) ≥75% of contig length with ≥1 × coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically developed for metagenomes provided the best estimates. Conclusions: These simulations provide benchmarks for selecting analysis cut-offs and establish that an optimized sample-to-ecological-inference viromics pipeline is robust for making ecological inferences from natural viral communities. Continued development to better accessing RNA, rare, and/or diverse viral populations and improved reference viral genome availability will alleviate many of viromics remaining limitations.},
doi = {10.7717/peerj.3817},
journal = {PeerJ},
number = ,
volume = 5,
place = {United States},
year = {Thu Sep 21 00:00:00 EDT 2017},
month = {Thu Sep 21 00:00:00 EDT 2017}
}
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Works referenced in this record:
Rising to the challenge: accelerated pace of discovery transforms marine virology
journal, February 2015
- Brum, Jennifer R.; Sullivan, Matthew B.
- Nature Reviews Microbiology, Vol. 13, Issue 3
The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes
journal, December 2009
- Angly, Florent E.; Willner, Dana; Prieto-Davó, Alejandra
- PLoS Computational Biology, Vol. 5, Issue 12
Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies
journal, April 2017
- Greenwald, William W.; Klitgord, Niels; Seguritan, Victor
- BMC Genomics, Vol. 18, Issue 1
Recombination and microdiversity in coastal marine cyanophages
journal, November 2009
- Marston, Marcia F.; Amrich, Christopher G.
- Environmental Microbiology, Vol. 11, Issue 11
Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains
journal, January 2013
- Doll, Hannah M.; Armitage, David W.; Daly, Rebecca A.
- BMC Microbiology, Vol. 13, Issue 1
Assembly of Viral Metagenomes from Yellowstone Hot Springs
journal, April 2008
- Schoenfeld, T.; Patterson, M.; Richardson, P. M.
- Applied and Environmental Microbiology, Vol. 74, Issue 13
Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
journal, February 2015
- Sharon, Itai; Kertesz, Michael; Hug, Laura A.
- Genome Research, Vol. 25, Issue 4
Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome
journal, August 2014
- Hurwitz, Bonnie L.; Brum, Jennifer R.; Sullivan, Matthew B.
- The ISME Journal, Vol. 9, Issue 2
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 35, Issue 8
Evaluation of viral genome assembly and diversity estimation in deep metagenomes
journal, January 2014
- Aguirre de Cárcer, Daniel; Angly, Florent E.; Alcamí, Antonio
- BMC Genomics, Vol. 15, Issue 1
Seasonality and monthly dynamics of marine myovirus communities: Marine myovirus community dynamics at SPOT
journal, April 2012
- Chow, Cheryl-Emiliane T.; Fuhrman, Jed A.
- Environmental Microbiology, Vol. 14, Issue 8
Recovering complete and draft population genomes from metagenome datasets
journal, March 2016
- Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack A.
- Microbiome, Vol. 4, Issue 1
Viruses as Winners in the Game of Life
journal, September 2016
- Cobián Güemes, Ana Georgina; Youle, Merry; Cantú, Vito Adrian
- Annual Review of Virology, Vol. 3, Issue 1
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
journal, August 2012
- Sharon, I.; Morowitz, M. J.; Thomas, B. C.
- Genome Research, Vol. 23, Issue 1
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
journal, November 2016
- Gregory, Ann C.; Solonenko, Sergei A.; Ignacio-Espinoza, J. Cesar
- BMC Genomics, Vol. 17, Issue 1
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
journal, September 2012
- Wrighton, K. C.; Thomas, B. C.; Sharon, I.
- Science, Vol. 337, Issue 6102
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method: Linker amplification for ultra-low DNA samples
journal, June 2012
- Duhaime, Melissa B.; Deng, Li; Poulos, Bonnie T.
- Environmental Microbiology, Vol. 14, Issue 9
Differential expression analysis for sequence count data
journal, October 2010
- Anders, Simon; Huber, Wolfgang
- Genome Biology, Vol. 11, Issue 10
Using ecological diversity measures with bacterial communities
journal, February 2003
- Hill, Tom C. J.; Walsh, Kerry A.; Harris, James A.
- FEMS Microbiology Ecology, Vol. 43, Issue 1
Challenges in the analysis of viral metagenomes
journal, July 2016
- Rose, Rebecca; Constantinides, Bede; Tapinos, Avraam
- Virus Evolution, Vol. 2, Issue 2
Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014
- Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern
- Bioinformatics, Vol. 30, Issue 15
Patterns and ecological drivers of ocean viral communities
journal, May 2015
- Brum, J. R.; Ignacio-Espinoza, J. C.; Roux, S.
- Science, Vol. 348, Issue 6237
Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR
journal, June 2011
- Tadmor, A. D.; Ottesen, E. A.; Leadbetter, J. R.
- Science, Vol. 333, Issue 6038
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
journal, April 2014
- McMurdie, Paul J.; Holmes, Susan
- PLoS Computational Biology, Vol. 10, Issue 4
The khmer software package: enabling efficient nucleotide sequence analysis
journal, January 2015
- Crusoe, Michael R.; Alameldin, Hussien F.; Awad, Sherine
- F1000Research, Vol. 4
Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
journal, January 2017
- Vollmers, John; Wiegand, Sandra; Kaster, Anne-Kristin
- PLOS ONE, Vol. 12, Issue 1
Where Next for Microbiome Research?
journal, January 2015
- Waldor, Matthew K.; Tyson, Gene; Borenstein, Elhanan
- PLOS Biology, Vol. 13, Issue 1
Assessing the Impact of Assemblers on Virus Detection in a De Novo Metagenomic Analysis Pipeline
journal, September 2017
- White, Daniel J.; Wang, Jing; Hall, Richard J.
- Journal of Computational Biology, Vol. 24, Issue 9
Towards quantitative viromics for both double-stranded and single-stranded DNA viruses
journal, January 2016
- Roux, Simon; Solonenko, Natalie E.; Dang, Vinh T.
- PeerJ, Vol. 4
Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes
journal, May 2015
- Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia
- Frontiers in Microbiology, Vol. 6
metaSPAdes: a new versatile metagenomic assembler
journal, March 2017
- Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton
- Genome Research, Vol. 27, Issue 5
Single-virus genomics reveals hidden cosmopolitan and abundant viruses
journal, June 2017
- Martinez-Hernandez, Francisco; Fornas, Oscar; Lluesma Gomez, Monica
- Nature Communications, Vol. 8, Issue 1
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
journal, February 2012
- Mende, Daniel R.; Waller, Alison S.; Sunagawa, Shinichi
- PLoS ONE, Vol. 7, Issue 2
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
journal, July 2012
- Namiki, Toshiaki; Hachiya, Tsuyoshi; Tanaka, Hideaki
- Nucleic Acids Research, Vol. 40, Issue 20
Pyrosequencing enumerates and contrasts soil microbial diversity
journal, July 2007
- Roesch, Luiz F. W.; Fulthorpe, Roberta R.; Riva, Alberto
- The ISME Journal, Vol. 1, Issue 4
Are we missing half of the viruses in the ocean?
journal, November 2012
- Steward, Grieg F.; Culley, Alexander I.; Mueller, Jaclyn A.
- The ISME Journal, Vol. 7, Issue 3
Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics
journal, March 2012
- Roux, Simon; Enault, Francois; Robin, Agnès
- PLoS ONE, Vol. 7, Issue 3
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
Metabolic reprogramming by viruses in the sunlit and dark ocean
journal, January 2013
- Hurwitz, Bonnie L.; Hallam, Steven J.; Sullivan, Matthew B.
- Genome Biology, Vol. 14, Issue 11
MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
journal, June 2016
- Li, Dinghua; Luo, Ruibang; Liu, Chi-Man
- Methods, Vol. 102
Using MUMmer to Identify Similar Regions in Large Sequence Sets
journal, January 2003
- Delcher, Arthur L.; Salzberg, Steven L.; Phillippy, Adam M.
- Current Protocols in Bioinformatics, Vol. 00, Issue 1
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
journal, October 2016
- Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 45, Issue D1
Omega: an Overlap-graph de novo Assembler for Metagenomics
journal, June 2014
- Haider, Bahlul; Ahn, Tae-Hyuk; Bushnell, Brian
- Bioinformatics, Vol. 30, Issue 19
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012
- Peng, Y.; Leung, H. C. M.; Yiu, S. M.
- Bioinformatics, Vol. 28, Issue 11
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
journal, January 2014
- Vázquez-Castellanos, Jorge F.; García-López, Rodrigo; Pérez-Brocal, Vicente
- BMC Genomics, Vol. 15, Issue 1
Viral metagenomics
journal, May 2005
- Edwards, Robert A.; Rohwer, Forest
- Nature Reviews Microbiology, Vol. 3, Issue 6
Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere
journal, August 2005
- Filee, J.; Tetart, F.; Suttle, C. A.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 35
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
journal, November 2009
- Robinson, M. D.; McCarthy, D. J.; Smyth, G. K.
- Bioinformatics, Vol. 26, Issue 1
Distantly sampled soils carry few species in common
journal, June 2008
- Fulthorpe, Roberta R.; Roesch, Luiz F. W.; Riva, Alberto
- The ISME Journal, Vol. 2, Issue 9
NeSSM: A Next-Generation Sequencing Simulator for Metagenomics
journal, October 2013
- Jia, Ben; Xuan, Liming; Cai, Kaiye
- PLoS ONE, Vol. 8, Issue 10
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities: Using
journal, September 2013
- Logares, Ramiro; Sunagawa, Shinichi; Salazar, Guillem
- Environmental Microbiology, Vol. 16, Issue 9
Metavir 2: new tools for viral metagenome comparison and assembled virome analysis
journal, January 2014
- Roux, Simon; Tournayre, Jeremy; Mahul, Antoine
- BMC Bioinformatics, Vol. 15, Issue 1
A survey of error-correction methods for next-generation sequencing
journal, April 2012
- Yang, X.; Chockalingam, S. P.; Aluru, S.
- Briefings in Bioinformatics, Vol. 14, Issue 1
Robust estimation of microbial diversity in theory and in practice
journal, February 2013
- Haegeman, Bart; Hamelin, Jérôme; Moriarty, John
- The ISME Journal, Vol. 7, Issue 6
Differential abundance analysis for microbial marker-gene surveys
journal, September 2013
- Paulson, Joseph N.; Stine, O. Colin; Bravo, Héctor Corrada
- Nature Methods, Vol. 10, Issue 12
The bright side of microbial dark matter: lessons learned from the uncultivated majority
journal, June 2016
- Solden, Lindsey; Lloyd, Karen; Wrighton, Kelly
- Current Opinion in Microbiology, Vol. 31
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
journal, January 2017
- Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem
- PeerJ, Vol. 5
Microbes do not follow the elevational diversity patterns of plants and animals
journal, April 2011
- Fierer, Noah; McCain, Christy M.; Meir, Patrick
- Ecology, Vol. 92, Issue 4
Unveiling viral–host interactions within the ‘microbial dark matter’
journal, August 2014
- Martínez-García, Manuel; Santos, Fernando; Moreno-Paz, Mercedes
- Nature Communications, Vol. 5, Issue 1
Viral and microbial community dynamics in four aquatic environments
journal, February 2010
- Rodriguez-Brito, Beltran; Li, LinLin; Wegley, Linda
- The ISME Journal, Vol. 4, Issue 6
Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses: phageFISH - visualizing intracellular and free viruses
journal, March 2013
- Allers, Elke; Moraru, Cristina; Duhaime, Melissa B.
- Environmental Microbiology, Vol. 15, Issue 8
The Microbial Engines That Drive Earth's Biogeochemical Cycles
journal, May 2008
- Falkowski, P. G.; Fenchel, T.; Delong, E. F.
- Science, Vol. 320, Issue 5879
Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations
journal, September 2015
- García-López, Rodrigo; Vázquez-Castellanos, Jorge Francisco; Moya, Andrés
- Frontiers in Bioengineering and Biotechnology, Vol. 3
Genomic diversification of marine cyanophages into stable ecotypes: Cyanophage diversification into ecotypes
journal, October 2016
- Marston, Marcia F.; Martiny, Jennifer B. H.
- Environmental Microbiology, Vol. 18, Issue 11
Transcriptomic analysis of female and male gonads in juvenile snakeskin gourami (Trichopodus pectoralis)
journal, March 2020
- Boonanuntanasarn, Surintorn; Jangprai, Araya; Na-Nakorn, Uthairat
- Scientific Reports, Vol. 10, Issue 1
Characterization and functional analysis of phytoene synthase gene family in tobacco
journal, January 2021
- Wang, Zhaojun; Zhang, Lin; Dong, Chen
- BMC Plant Biology, Vol. 21, Issue 1
Assessing the impact of assemblers on virus detection in a de novo metagenomic analysis pipeline
text, January 2019
- White, Daniel J.; Wang, Jing; Hall, Richard J.
- Figshare
Differential expression analysis for sequence count data
journal, April 2010
- Anders, Simon; Huber, Wolfgang
- Nature Precedings
Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissible
text, January 2013
- McMurdie, Paul J.; Holmes, Susan
- arXiv
Using MUMmer to Identify Similar Regions in Large Sequence Sets
journal, January 2003
- Delcher, Arthur L.; Salzberg, Steven L.; Phillippy, Adam M.
- Current Protocols in Bioinformatics, Vol. 00, Issue 1
Salinimonas marina sp. nov. Isolated from Jeju Island Marine Sediment
journal, June 2021
- Kim, Minji; Lee, Ki-Eun; Cha, In-Tae
- Current Microbiology, Vol. 78, Issue 8
Binning Metagenomic Contigs Using Unsupervised Clustering and Reference Databases
journal, May 2022
- Jiang, Zhongjun; Li, Xiaobo; Guo, Lijun
- Interdisciplinary Sciences: Computational Life Sciences, Vol. 14, Issue 4
The bright side of microbial dark matter: lessons learned from the uncultivated majority
journal, June 2016
- Solden, Lindsey; Lloyd, Karen; Wrighton, Kelly
- Current Opinion in Microbiology, Vol. 31
MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
journal, June 2016
- Li, Dinghua; Luo, Ruibang; Liu, Chi-Man
- Methods, Vol. 102
Distantly sampled soils carry few species in common
journal, June 2008
- Fulthorpe, Roberta R.; Roesch, Luiz F. W.; Riva, Alberto
- The ISME Journal, Vol. 2, Issue 9
Viral and microbial community dynamics in four aquatic environments
journal, February 2010
- Rodriguez-Brito, Beltran; Li, LinLin; Wegley, Linda
- The ISME Journal, Vol. 4, Issue 6
Are we missing half of the viruses in the ocean?
journal, November 2012
- Steward, Grieg F.; Culley, Alexander I.; Mueller, Jaclyn A.
- The ISME Journal, Vol. 7, Issue 3
Robust estimation of microbial diversity in theory and in practice
journal, February 2013
- Haegeman, Bart; Hamelin, Jérôme; Moriarty, John
- The ISME Journal, Vol. 7, Issue 6
Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome
journal, August 2014
- Hurwitz, Bonnie L.; Brum, Jennifer R.; Sullivan, Matthew B.
- The ISME Journal, Vol. 9, Issue 2
Single-virus genomics reveals hidden cosmopolitan and abundant viruses
journal, June 2017
- Martinez-Hernandez, Francisco; Fornas, Oscar; Lluesma Gomez, Monica
- Nature Communications, Vol. 8, Issue 1
Unveiling viral–host interactions within the ‘microbial dark matter’
journal, August 2014
- Martínez-García, Manuel; Santos, Fernando; Moreno-Paz, Mercedes
- Nature Communications, Vol. 5, Issue 1
Differential expression analysis for sequence count data
journal, April 2010
- Anders, Simon; Huber, Wolfgang
- Nature Precedings
CXCR4 signaling directs Igk recombination and the molecular mechanisms of late B lymphopoiesis
journal, September 2019
- Mandal, Malay; Okoreeh, Michael K.; Kennedy, Domenick E.
- Nature Immunology, Vol. 20, Issue 10
Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain
journal, January 2020
- Raldúa, Demetrio; Casado, Marta; Prats, Eva
- Scientific Reports, Vol. 10, Issue 1
Intestinal bacteria flora changes in patients with Mycoplasma pneumoniae pneumonia with or without wheezing
journal, April 2022
- Jiang, Yonghong; Bao, Chunxiu; Zhao, Xiaoyang
- Scientific Reports, Vol. 12, Issue 1
Salinity tolerance mechanisms of an Arctic Pelagophyte using comparative transcriptomic and gene expression analysis
journal, May 2022
- Freyria, Nastasia J.; Kuo, Alan; Chovatia, Mansi
- Communications Biology, Vol. 5, Issue 1
Assessing the Impact of Assemblers on Virus Detection in a De Novo Metagenomic Analysis Pipeline
journal, September 2017
- White, Daniel J.; Wang, Jing; Hall, Richard J.
- Journal of Computational Biology, Vol. 24, Issue 9
A survey of error-correction methods for next-generation sequencing
journal, April 2012
- Yang, X.; Chockalingam, S. P.; Aluru, S.
- Briefings in Bioinformatics, Vol. 14, Issue 1
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
journal, November 2009
- Robinson, M. D.; McCarthy, D. J.; Smyth, G. K.
- Bioinformatics, Vol. 26, Issue 1
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012
- Peng, Y.; Leung, H. C. M.; Yiu, S. M.
- Bioinformatics, Vol. 28, Issue 11
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
journal, July 2012
- Namiki, Toshiaki; Hachiya, Tsuyoshi; Tanaka, Hideaki
- Nucleic Acids Research, Vol. 40, Issue 20
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
journal, October 2016
- Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 45, Issue D1
Challenges in the analysis of viral metagenomes
journal, July 2016
- Rose, Rebecca; Constantinides, Bede; Tapinos, Avraam
- Virus Evolution, Vol. 2, Issue 2
Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses: phageFISH - visualizing intracellular and free viruses
journal, March 2013
- Allers, Elke; Moraru, Cristina; Duhaime, Melissa B.
- Environmental Microbiology, Vol. 15, Issue 8
Recombination and microdiversity in coastal marine cyanophages
journal, November 2009
- Marston, Marcia F.; Amrich, Christopher G.
- Environmental Microbiology, Vol. 11, Issue 11
Seasonality and monthly dynamics of marine myovirus communities: Marine myovirus community dynamics at SPOT
journal, April 2012
- Chow, Cheryl-Emiliane T.; Fuhrman, Jed A.
- Environmental Microbiology, Vol. 14, Issue 8
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method: Linker amplification for ultra-low DNA samples
journal, June 2012
- Duhaime, Melissa B.; Deng, Li; Poulos, Bonnie T.
- Environmental Microbiology, Vol. 14, Issue 9
Patterns and ecological drivers of ocean viral communities
journal, May 2015
- Brum, J. R.; Ignacio-Espinoza, J. C.; Roux, S.
- Science, Vol. 348, Issue 6237
Development of phoH as a Novel Signature Gene for Assessing Marine Phage Diversity
journal, September 2011
- Goldsmith, Dawn B.; Crosti, Giuseppe; Dwivedi, Bhakti
- Applied and Environmental Microbiology, Vol. 77, Issue 21
New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily
journal, January 2014
- Trame, Christine B.; Chang, Yuanyuan; Axelrod, Herbert L.
- BMC Bioinformatics, Vol. 15, Issue 1
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
journal, January 2014
- Vázquez-Castellanos, Jorge F.; García-López, Rodrigo; Pérez-Brocal, Vicente
- BMC Genomics, Vol. 15, Issue 1
Evaluation of viral genome assembly and diversity estimation in deep metagenomes
journal, January 2014
- Aguirre de Cárcer, Daniel; Angly, Florent E.; Alcamí, Antonio
- BMC Genomics, Vol. 15, Issue 1
Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains
journal, January 2013
- Doll, Hannah M.; Armitage, David W.; Daly, Rebecca A.
- BMC Microbiology, Vol. 13, Issue 1
Metabolic reprogramming by viruses in the sunlit and dark ocean
journal, January 2013
- Hurwitz, Bonnie L.; Hallam, Steven J.; Sullivan, Matthew B.
- Genome Biology, Vol. 14, Issue 11
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
journal, November 2016
- Gregory, Ann C.; Solonenko, Sergei A.; Ignacio-Espinoza, J. Cesar
- BMC Genomics, Vol. 17, Issue 1
Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies
journal, April 2017
- Greenwald, William W.; Klitgord, Niels; Seguritan, Victor
- BMC Genomics, Vol. 18, Issue 1
The khmer software package: enabling efficient nucleotide sequence analysis
journal, January 2015
- Crusoe, Michael R.; Alameldin, Hussien F.; Awad, Sherine
- F1000Research, Vol. 4
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
journal, February 2012
- Mende, Daniel R.; Waller, Alison S.; Sunagawa, Shinichi
- PLoS ONE, Vol. 7, Issue 2
Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics
journal, March 2012
- Roux, Simon; Enault, Francois; Robin, Agnès
- PLoS ONE, Vol. 7, Issue 3
NeSSM: A Next-Generation Sequencing Simulator for Metagenomics
journal, October 2013
- Jia, Ben; Xuan, Liming; Cai, Kaiye
- PLoS ONE, Vol. 8, Issue 10
Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
journal, January 2017
- Vollmers, John; Wiegand, Sandra; Kaster, Anne-Kristin
- PLOS ONE, Vol. 12, Issue 1
Microbes do not follow the elevational diversity patterns of plants and animals
journal, April 2011
- Fierer, Noah; McCain, Christy M.; Meir, Patrick
- Ecology, Vol. 92, Issue 4
Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations
journal, September 2015
- García-López, Rodrigo; Vázquez-Castellanos, Jorge Francisco; Moya, Andrés
- Frontiers in Bioengineering and Biotechnology, Vol. 3
Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissible
text, January 2013
- McMurdie, Paul J.; Holmes, Susan
- arXiv
Works referencing / citing this record:
Mini‐Metagenomics and Nucleotide Composition Aid the Identification and Host Association of Novel Bacteriophage Sequences
journal, May 2019
- Deaton, Jonathan; Yu, Feiqiao Brian; Quake, Stephen R.
- Advanced Biosystems, Vol. 3, Issue 11
The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific
journal, October 2019
- Shkoporov, Andrey N.; Clooney, Adam G.; Sutton, Thomas D. S.
- Cell Host & Microbe, Vol. 26, Issue 4
Minimum Information about an Uncultivated Virus Genome (MIUViG)
journal, December 2018
- Roux, Simon; Adriaenssens, Evelien M.; Dutilh, Bas E.
- Nature Biotechnology, Vol. 37, Issue 1
Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean
journal, September 2018
- Martinez-Hernandez, Francisco; Fornas, Òscar; Lluesma Gomez, Monica
- The ISME Journal, Vol. 13, Issue 1
Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems
journal, February 2019
- Bischoff, Vera; Bunk, Boyke; Meier-Kolthoff, Jan P.
- The ISME Journal, Vol. 13, Issue 6
Murine colitis reveals a disease-associated bacteriophage community
journal, July 2018
- Duerkop, Breck A.; Kleiner, Manuel; Paez-Espino, David
- Nature Microbiology, Vol. 3, Issue 9
Next-generation sequencing of dsRNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO
journal, November 2019
- Wilcox, Alexander H.; Delwart, Eric; Díaz-Muñoz, Samuel L.
- Microbial Genomics, Vol. 5, Issue 11
Riding the wave of genomics to investigate aquatic coliphage diversity and activity
journal, April 2019
- Michniewski, Slawomir; Redgwell, Tamsin; Grigonyte, Aurelija
- Environmental Microbiology, Vol. 21, Issue 6
Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake
journal, September 2019
- Okazaki, Yusuke; Nishimura, Yosuke; Yoshida, Takashi
- Environmental Microbiology, Vol. 21, Issue 12
Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341
journal, July 2019
- Nilsson, E.; Li, K.; Fridlund, J.
- Applied and Environmental Microbiology, Vol. 85, Issue 18
A Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”
journal, May 2019
- Roux, Simon
- mSystems, Vol. 4, Issue 3
Host-hijacking and planktonic piracy: how phages command the microbial high seas
journal, February 2019
- Warwick-Dugdale, Joanna; Buchholz, Holger H.; Allen, Michael J.
- Virology Journal, Vol. 16, Issue 1
Choice of assembly software has a critical impact on virome characterisation
journal, January 2019
- Sutton, Thomas D. S.; Clooney, Adam G.; Ryan, Feargal J.
- Microbiome, Vol. 7, Issue 1
MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
journal, August 2018
- Amgarten, Deyvid; Braga, Lucas P. P.; da Silva, Aline M.
- Frontiers in Genetics, Vol. 9
Deciphering the Human Virome with Single-Virus Genomics and Metagenomics
journal, March 2018
- de la Cruz Peña, Maria; Martinez-Hernandez, Francisco; Garcia-Heredia, Inmaculada
- Viruses, Vol. 10, Issue 3
Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions
journal, September 2018
- Coy, Samantha; Gann, Eric; Pound, Helena
- Viruses, Vol. 10, Issue 9
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
journal, January 2019
- Warwick-Dugdale, Joanna; Solonenko, Natalie; Moore, Karen
- PeerJ, Vol. 7
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
journal, January 2019
- Trubl, Gareth; Roux, Simon; Solonenko, Natalie
- PeerJ, Vol. 7
Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
journal, January 2019
- Bekliz, Meriem; Brandani, Jade; Bourquin, Massimo
- PeerJ, Vol. 7
Mouse Vendor Influence on the Bacterial and Viral Gut Composition Exceeds the Effect of Diet
journal, May 2019
- Rasmussen, Torben Sølbeck; de Vries, Liv; Kot, Witold
- Viruses, Vol. 11, Issue 5
Minimum information about an uncultivated virus genome (MIUVIG)
text, January 2019
- Roux, Simon; Adriaenssens, Evelien M.; Dutilh, Bas E.
- ETH Zurich
KBase Narrative - Viral Analysis End-to-End
dataset, January 2022
- Bolduc, Benjamin
- U.S. Department of Energy Systems Biology Knowledgebase
Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems
journal, February 2019
- Bischoff, Vera; Bunk, Boyke; Meier-Kolthoff, Jan P.
- The ISME Journal, Vol. 13, Issue 6
Murine colitis reveals a disease-associated bacteriophage community
journal, July 2018
- Duerkop, Breck A.; Kleiner, Manuel; Paez-Espino, David
- Nature Microbiology, Vol. 3, Issue 9
Riding the wave of genomics to investigate aquatic coliphage diversity and activity
journal, April 2019
- Michniewski, Slawomir; Redgwell, Tamsin; Grigonyte, Aurelija
- Environmental Microbiology, Vol. 21, Issue 6