Cargando…

RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing

Despite the advent of third-generation sequencing technologies, modern bacterial ecology studies still use Illumina to sequence small (~400 bp) hypervariable regions of the 16S rRNA SSU for phylogenetic classification. By sequencing a larger region of the rRNA gene operons, the limitations and biase...

Descripción completa

Detalles Bibliográficos
Autores principales:	Petrone, Joseph R., Rios Glusberger, Paula, George, Christian D., Milletich, Patricia L., Ahrens, Angelica P., Roesch, Luiz Fernando Wurdig, Triplett, Eric W.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Frontiers Media S.A. 2023
Materias:	Microbiology
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10402275/ https://www.ncbi.nlm.nih.gov/pubmed/37547696 http://dx.doi.org/10.3389/fmicb.2023.1201064

Ejemplares similares

Unamplified, Long-Read Metagenomic Sequencing Approach to Close Endosymbiont Genomes of Low-Biomass Insect Populations
por: Petrone, Joseph R., et al.
Publicado: (2022)

MinION™ Nanopore Sequencing of Skin Microbiome 16S and 16S-23S rRNA Gene Amplicons
por: Rozas, Miquel, et al.
Publicado: (2022)

NanoRTax, a real-time pipeline for taxonomic and diversity analysis of nanopore 16S rRNA amplicon sequencing data
por: Rodríguez-Pérez, Héctor, et al.
Publicado: (2022)

Gut microbiome markers in subgroups of HLA class II genotyped infants signal future celiac disease in the general population: ABIS study
por: Milletich, Patricia L., et al.
Publicado: (2022)

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon
por: Cuscó, Anna, et al.
Publicado: (2019)

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

Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing
por: Abellan-Schneyder, Isabel, et al.
Publicado: (2021)

De novo species identification using 16S rRNA gene nanopore sequencing
por: Angell, Inga Leena, et al.
Publicado: (2020)

16S rRNA nanopore sequencing for the diagnosis of ocular infection: a feasibility study
por: Omi, Masatoshi, et al.
Publicado: (2022)

Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S‐ITS‐23S rRNA operon
por: Martijn, Joran, et al.
Publicado: (2019)

Benchmarking assembly free nanopore read mappers to classify complex millipede gut microbiota via Oxford Nanopore Sequencing Technology
por: Geli-Cruz, Orlando J., et al.
Publicado: (2023)

16S-FASAS: an integrated pipeline for synthetic full-length 16S rRNA gene sequencing data analysis
por: Zhang, Ke, et al.
Publicado: (2022)

Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota
por: Heikema, Astrid P., et al.
Publicado: (2020)

Identification of Escherichia coli through analysis of 16S rRNA and 16S-23S rRNA internal transcribed spacer region sequences
por: Magray, Mohammed Siraj Ud Din, et al.
Publicado: (2011)

BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons
por: Djemiel, Christophe, et al.
Publicado: (2020)

Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals
por: Celis, Arianna I., et al.
Publicado: (2022)

MAECI: A pipeline for generating consensus sequence with nanopore sequencing long-read assembly and error correction
por: Lang, Jidong
Publicado: (2022)

Improving the Diagnosis of Bacterial Infections: Evaluation of 16S rRNA Nanopore Metagenomics in Culture-Negative Samples
por: Bouchiat, Coralie, et al.
Publicado: (2022)

SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis
por: Zorz, Jackie, et al.
Publicado: (2023)

16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets
por: Chaudhary, Nikhil, et al.
Publicado: (2015)

Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples
por: Barb, Jennifer J., et al.
Publicado: (2016)

Pipeline for amplifying and analyzing amplicons of the V1–V3 region of the 16S rRNA gene
por: Allen, Heather K., et al.
Publicado: (2016)

A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis
por: Whelan, Fiona J., et al.
Publicado: (2017)

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples
por: Gonzalez, Emmanuel, et al.
Publicado: (2019)

Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing
por: Langsiri, Nattapong, et al.
Publicado: (2023)

Development of an efficient antimicrobial susceptibility testing method with species identification by Nanopore sequencing of 16S rRNA amplicons
por: Kawai, Yuto, et al.
Publicado: (2022)

Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing
por: Lee, Annie Wing-Tung, et al.
Publicado: (2023)

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons
por: Lagkouvardos, Ilias, et al.
Publicado: (2017)

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
por: Straub, Daniel, et al.
Publicado: (2020)

Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing
por: Welham, Zoe, et al.
Publicado: (2023)

Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer
por: Benítez-Páez, Alfonso, et al.
Publicado: (2016)

Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer
por: Kai, Shinichi, et al.
Publicado: (2019)

Mechanisms behind variation in the Clostridium difficile 16S–23S rRNA intergenic spacer region
por: Indra, Alexander, et al.
Publicado: (2010)

Recombination Drives Evolution of the Clostridium difficile 16S-23S rRNA Intergenic Spacer Region
por: Janezic, Sandra, et al.
Publicado: (2014)

Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing
por: Smith, Andrew M., et al.
Publicado: (2019)

NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
por: Ramiro-Garcia, Javier, et al.
Publicado: (2018)

Comparison of Bioinformatics Pipelines and Operating Systems for the Analyses of 16S rRNA Gene Amplicon Sequences in Human Fecal Samples
por: Marizzoni, Moira, et al.
Publicado: (2020)

A streamlined pipeline based on HmmUFOtu for microbial community profiling using 16S rRNA amplicon sequencing
por: Kim, Hyeonwoo, et al.
Publicado: (2023)

Pyrosequence Read Length of 16S rRNA Gene Affects Phylogenetic Assignment of Plant-associated Bacteria
por: Okubo, Takashi, et al.
Publicado: (2012)

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

Cannot write session to /tmp/vufind_sessions/sess_2at603el8cm495p7sd464h3jm0