Cargando…

VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing

BACKGROUND: The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary relationships among taxa are inferred by a phylogenetic tree. Thus, the combined...

Descripción completa

Detalles Bibliográficos
Autores principales:	Mori, Hiroshi, Maruyama, Takayuki, Yano, Masahiro, Yamada, Takuji, Kurokawa, Ken
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2018
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861490/ https://www.ncbi.nlm.nih.gov/pubmed/29560821 http://dx.doi.org/10.1186/s12918-018-0545-2

Ejemplares similares

VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences
por: Mori, Hiroshi, et al.
Publicado: (2010)

CLAST: CUDA implemented large-scale alignment search tool
por: Yano, Masahiro, et al.
Publicado: (2014)

MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing
por: Parikh, Hardik I., et al.
Publicado: (2016)

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics
por: Arıkan, Muzaffer, et al.
Publicado: (2020)

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis
por: Ferravante, Carlo, et al.
Publicado: (2021)

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
por: Xie, Chao, et al.
Publicado: (2016)

Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences
por: Ong, Swee Hoe, et al.
Publicado: (2013)

Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data
por: Brumfield, Kyle D., et al.
Publicado: (2020)

Microbial diversity of a full‐scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing
por: Delforno, Tiago Palladino, et al.
Publicado: (2017)

Multicenter assessment of microbial community profiling using 16S rRNA gene sequencing and shotgun metagenomic sequencing
por: Han, Dongsheng, et al.
Publicado: (2020)

Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data
por: Pereira-Flores, Emiliano, et al.
Publicado: (2019)

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing
por: Prodan, Andrei, et al.
Publicado: (2020)

Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing
por: Mehetre, Gajanan T., et al.
Publicado: (2016)

SPINGO: a rapid species-classifier for microbial amplicon sequences
por: Allard, Guy, et al.
Publicado: (2015)

Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
por: Tessler, Michael, et al.
Publicado: (2017)

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data
por: Devlin, Joseph C., et al.
Publicado: (2018)

Salivary Microbiome in Adenoid Cystic Carcinoma Detected by 16S rRNA Sequencing and Shotgun Metagenomics
por: Jiang, Qian, et al.
Publicado: (2021)

Séance: reference-based phylogenetic analysis for 18S rRNA studies
por: Medlar, Alan, et al.
Publicado: (2014)

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
por: Meyer, F, et al.
Publicado: (2008)

Microbial Diversity in Commercial Bee Pollen from Europe, Chile, and Mexico, Based on 16S rRNA Gene Amplicon Metagenome Sequencing
por: Moreno Andrade, Vicente D., et al.
Publicado: (2018)

CAMISIM: simulating metagenomes and microbial communities
por: Fritz, Adrian, et al.
Publicado: (2019)

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

Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies
por: Usyk, Mykhaylo, et al.
Publicado: (2023)

Shotgun metagenomics captures more microbial diversity than targeted 16S rRNA gene sequencing for field specimens and preserved museum specimens
por: Madison, Joseph D., et al.
Publicado: (2023)

Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies
por: Wang, Yong, et al.
Publicado: (2009)

Looking for Rhizobacterial Ecological Indicators in Agricultural Soils Using 16S rRNA metagenomic Amplicon Data
por: Valverde, José R., et al.
Publicado: (2016)

RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes
por: Zhang, Yanming, et al.
Publicado: (2016)

Long-Read 16S rRNA Amplicon and Metagenomic Data of Swine Feed-Additive Probiotics Product
por: Sudjai, Aunthikarn, et al.
Publicado: (2022)

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing
por: Thiel, Vera, et al.
Publicado: (2016)

Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing
por: Chan, Chia Sing, et al.
Publicado: (2015)

Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections
por: Lamoureux, Claudie, et al.
Publicado: (2022)

Evaluating Established Methods for Rumen 16S rRNA Amplicon Sequencing With Mock Microbial Populations
por: McGovern, Emily, et al.
Publicado: (2018)

16S rRNA Amplicon Sequencing of Microbial Biofilms from Marsberg Copper Mine, Germany
por: Arif, Sania, et al.
Publicado: (2021)

MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles
por: Shaw, Grace Tzun-Wen, et al.
Publicado: (2016)

Metagenomic 16S rRNA amplicon data of gut microbial diversity in three species of subterranean termites (Coptotermes gestroi, Globitermes sulphureus and Macrotermes gilvus)
por: Shamsuri, Qurratu'Aini Syasya, et al.
Publicado: (2023)

HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies
por: Zheng, Qi, et al.
Publicado: (2018)

Comparison of the Microbiome of Artisanal Homemade and Industrial Feta Cheese through Amplicon Sequencing and Shotgun Metagenomics
por: Papadimitriou, Konstantinos, et al.
Publicado: (2022)

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities
por: Cottier, Fabien, et al.
Publicado: (2018)

Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing
por: Liu, Yuanfeng, et al.
Publicado: (2021)

Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics
por: Poretsky, Rachel, et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_seoe3ld629a2dq37mo2oa15h4l