Cargando…

Evaluating the Information Content of Shallow Shotgun Metagenomics

Although microbial communities are associated with human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes in such communities. While deep whole-metagenome shotgun (WMS) sequencing provides high taxonomic and functional res...

Descripción completa

Detalles Bibliográficos
Autores principales:	Hillmann, Benjamin, Al-Ghalith, Gabriel A., Shields-Cutler, Robin R., Zhu, Qiyun, Gohl, Daryl M., Beckman, Kenneth B., Knight, Rob, Knights, Dan
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	American Society for Microbiology 2018
Materias:	Methods and Protocols
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234283/ https://www.ncbi.nlm.nih.gov/pubmed/30443602 http://dx.doi.org/10.1128/mSystems.00069-18

Ejemplares similares

SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control
por: Al-Ghalith, Gabriel A., et al.
Publicado: (2018)

Two-Target Quantitative PCR To Predict Library Composition for Shallow Shotgun Sequencing
por: Cho, Matthew Y., et al.
Publicado: (2021)

synDNA—a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing
por: Zaramela, Livia S., et al.
Publicado: (2022)

METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses
por: Milani, Christian, et al.
Publicado: (2021)

DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing
por: Mendes, Catarina I., et al.
Publicado: (2020)

Taxonomic classification of metagenomic shotgun sequences with CARMA3
por: Gerlach, Wolfgang, et al.
Publicado: (2011)

Shallow shotgun sequencing reduces technical variation in microbiome analysis
por: La Reau, Alex J., et al.
Publicado: (2023)

Autometa: automated extraction of microbial genomes from individual shotgun metagenomes
por: Miller, Ian J, et al.
Publicado: (2019)

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies
por: Shields-Cutler, Robin R., et al.
Publicado: (2018)

An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs
por: Serghiou, Iliana R., et al.
Publicado: (2023)

Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
por: Cattonaro, Federica, et al.
Publicado: (2020)

Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification
por: Gohl, Daryl M., et al.
Publicado: (2019)

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

Calour: an Interactive, Microbe-Centric Analysis Tool
por: Xu, Zhenjiang Zech, et al.
Publicado: (2019)

DOE JGI Metagenome Workflow
por: Clum, Alicia, et al.
Publicado: (2021)

A breath of fresh air in microbiome science: shallow shotgun metagenomics for a reliable disentangling of microbial ecosystems
por: Lugli, Gabriele Andrea, et al.
Publicado: (2022)

Identification of fungi in shotgun metagenomics datasets
por: Donovan, Paul D., et al.
Publicado: (2018)

Deciphering Active Prophages from Metagenomes
por: Kieft, Kristopher, et al.
Publicado: (2022)

Derivation of HLA types from shotgun sequence datasets
por: Warren, René L, et al.
Publicado: (2012)

Finished bacterial genomes from shotgun sequence data
por: Ribeiro, Filipe J., et al.
Publicado: (2012)

Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution
por: Carr, Rogan, et al.
Publicado: (2013)

Dissecting and tuning primer editing by proofreading polymerases
por: Gohl, Daryl M, et al.
Publicado: (2021)

MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics
por: Churcheward, Benjamin, et al.
Publicado: (2022)

Characterization of Shallow Whole-Metagenome Shotgun Sequencing as a High-Accuracy and Low-Cost Method by Complicated Mock Microbiomes
por: Xu, Wenyi, et al.
Publicado: (2021)

Saliva Testing Is Accurate for Early-Stage and Presymptomatic COVID-19
por: Johnson, Abigail J., et al.
Publicado: (2021)

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
por: Sanders, Jon G., et al.
Publicado: (2019)

Metagenomic Sequencing for Identification of Xylella fastidiosa from Leaf Samples
por: Román-Reyna, Verónica, et al.
Publicado: (2021)

A standardized quantitative analysis strategy for stable isotope probing metagenomics
por: Vyshenska, Dariia, et al.
Publicado: (2023)

Background Filtering of Clinical Metagenomic Sequencing with a Library Concentration-Normalized Model
por: Du, Juan, et al.
Publicado: (2022)

Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes
por: Li, Yiming, et al.
Publicado: (2022)

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
por: Putnam, Nicholas H., et al.
Publicado: (2016)

VB(12)Path for Accurate Metagenomic Profiling of Microbially Driven Cobalamin Synthesis Pathways
por: Zhou, Jiayin, et al.
Publicado: (2021)

MetaPhage: an Automated Pipeline for Analyzing, Annotating, and Classifying Bacteriophages in Metagenomics Sequencing Data
por: Pandolfo, Mattia, et al.
Publicado: (2022)

An introduction to the analysis of shotgun metagenomic data
por: Sharpton, Thomas J.
Publicado: (2014)

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
por: Chapman, Jarrod A, et al.
Publicado: (2015)

Mining of unexplored habitats for novel chitinases—chiA as a helper gene proxy in metagenomics
por: Cretoiu, Mariana Silvia, et al.
Publicado: (2012)

Comparative assessment of methods for metagenomic DNA isolation from soils of different crop growing fields
por: Tanveer, Aiman, et al.
Publicado: (2016)

phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes
por: Gruber-Vodicka, Harald R., et al.
Publicado: (2020)

A rapid and efficient strategy to identify and recover biosynthetic gene clusters from soil metagenomes
por: Negri, Timo, et al.
Publicado: (2022)

Bygiene: The New Paradigm of Bidirectional Hygiene
por: Al-Ghalith, Gabriel A., et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_4kpacr4ldlcm0jviaicuknl7dh