Cargando…

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes

BACKGROUND: Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential. Reconstruction of DNA fragments into genomes from metagenomes (called met...

Descripción completa

Detalles Bibliográficos
Autores principales:	Papudeshi, Bhavya, Haggerty, J. Matthew, Doane, Michael, Morris, Megan M., Walsh, Kevin, Beattie, Douglas T., Pande, Dnyanada, Zaeri, Parisa, Silva, Genivaldo G. Z., Thompson, Fabiano, Edwards, Robert A., Dinsdale, Elizabeth A.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2017
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706307/ https://www.ncbi.nlm.nih.gov/pubmed/29183281 http://dx.doi.org/10.1186/s12864-017-4294-1

Ejemplares similares

Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera
por: Morris, Megan M., et al.
Publicado: (2016)

Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale
por: Lima, Laís F. O., et al.
Publicado: (2022)

Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network
por: Lima, Laís F. O., et al.
Publicado: (2020)

Aura-biomes are present in the water layer above coral reef benthic macro-organisms
por: Walsh, Kevin, et al.
Publicado: (2017)

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing
por: Lind, Abigail L., et al.
Publicado: (2021)

Epidermal Microbiomes of Leopard Sharks (Triakis semifasciata) Are Consistent across Captive and Wild Environments
por: Goodman, Asha Z., et al.
Publicado: (2022)

Rhodoliths holobionts in a changing ocean: host-microbes interactions mediate coralline algae resilience under ocean acidification
por: Cavalcanti, Giselle S., et al.
Publicado: (2018)

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community
por: Bowers, Robert M., et al.
Publicado: (2015)

Combining de novo and reference-guided assembly with scaffold_builder
por: Silva, Genivaldo GZ, et al.
Publicado: (2013)

Benchmarking different approaches for Norovirus genome assembly in metagenome samples
por: Fuentes-Trillo, Azahara, et al.
Publicado: (2021)

Phables: from fragmented assemblies to high-quality bacteriophage genomes
por: Mallawaarachchi, Vijini, et al.
Publicado: (2023)

Phables: from fragmented assemblies to high-quality bacteriophage genomes
por: Mallawaarachchi, Vijini, et al.
Publicado: (2023)

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
por: Ren, Jie, et al.
Publicado: (2017)

METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs
por: Zhang, Zhenmiao, et al.
Publicado: (2021)

An application of statistics to comparative metagenomics
por: Rodriguez-Brito, Beltran, et al.
Publicado: (2006)

Hill-based dissimilarity indices and null models for analysis of microbial community assembly
por: Modin, Oskar, et al.
Publicado: (2020)

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics
por: Goussarov, Gleb, et al.
Publicado: (2022)

The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge
por: Doane, Michael P., et al.
Publicado: (2020)

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
por: Yooseph, Shibu, et al.
Publicado: (2008)

A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes
por: Gkanogiannis, Anestis, et al.
Publicado: (2016)

In-depth resistome analysis by targeted metagenomics
por: Lanza, Val F., et al.
Publicado: (2018)

De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline
por: Lin, You-Yu, et al.
Publicado: (2017)

Feature selection for gene prediction in metagenomic fragments
por: Al-Ajlan, Amani, et al.
Publicado: (2018)

Stingray epidermal microbiomes are species-specific with local adaptations
por: Kerr, Emma N., et al.
Publicado: (2023)

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
por: Silva, Genivaldo Gueiros Z., et al.
Publicado: (2016)

Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy
por: Grigson, Susanna R, et al.
Publicado: (2023)

Network construction and structure detection with metagenomic count data
por: Liu, Zhenqiu, et al.
Publicado: (2015)

Reduced metagenome sequencing for strain-resolution taxonomic profiles
por: Snipen, Lars, et al.
Publicado: (2021)

Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption
por: Minich, Jeremiah J., et al.
Publicado: (2018)

Metagenomic Insights into Anaerobic Metabolism along an Arctic Peat Soil Profile
por: Lipson, David A., et al.
Publicado: (2013)

Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle
por: Silveira, Cynthia B., et al.
Publicado: (2017)

The Promise and Pitfalls of Prophages
por: McKerral, Jody C., et al.
Publicado: (2023)

Bacterial rose garden for metagenomic SNP-based phylogeny visualization
por: Alexeev, Dmitry, et al.
Publicado: (2015)

Improving saliva shotgun metagenomics by chemical host DNA depletion
por: Marotz, Clarisse A., et al.
Publicado: (2018)

Mining, analyzing, and integrating viral signals from metagenomic data
por: Zheng, Tingting, et al.
Publicado: (2019)

MetaDecoder: a novel method for clustering metagenomic contigs
por: Liu, Cong-Cong, et al.
Publicado: (2022)

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate
por: Walters, Kevin A., et al.
Publicado: (2022)

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares
por: Silva, Genivaldo Gueiros Z., et al.
Publicado: (2014)

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS
por: Fosso, Bruno, et al.
Publicado: (2015)

Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples
por: Lewandowska, Dagmara W., et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_bvesq147l3atf3pfemuhp5ttho