ArticleFrontiers in microbiology2017
Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp.
Article in Frontiers in microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
34 citing papers in PubMed.
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- Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.Environmental microbiome · 2024Article
- In search of the pH limit of growth in halo-alkaliphilic cyanobacteria.Environmental microbiology reports · 2024Article
- Coordinated proteome change precedes cell lysis and death in a mat-forming cyanobacterium.The ISME journal · 2023Article
- Frequency of change determines effectiveness of microbial response strategies.The ISME journal · 2023Article
- Identification of Eimeria spp. in domestic chickens raised in alternative poultry production systems in the State of São Paulo, Brazil.Revista brasileira de parasitologia veterinaria = Brazilian journal of veterinary parasitology : Orgao Oficial do Colegio Brasileiro de Parasitologia Veterinaria · 2023Article
- The Component and Functional Pathways of Gut Microbiota Are Altered in Populations with Poor Sleep Quality - A Preliminary Report.Polish journal of microbiology · 2022Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently.BMC bioinformatics · 2022Article
- Metabolic responses of thermophilic endospores to sudden heat-induced perturbation in marine sediment samples.Frontiers in microbiology · 2022Article
- Dynamic Evolution and Correlation between Metabolites and Microorganisms during Manufacturing Process and Storage of Fu Brick Tea.Metabolites · 2021Article
- Diesel and Crude Oil Biodegradation by Cold-Adapted Microbial Communities in the Labrador Sea.Applied and environmental microbiology · 2021Article
- Sasso Pisano Geothermal Field Environment Harbours DiverseMicroorganisms · 2021Article
- Ammonium Removal in Aquaponics Indicates Participation of Comammox Nitrospira.Current microbiology · 2021Article
- 16S rRNA Amplicon Sequencing of Microbial Biofilms from Marsberg Copper Mine, Germany.Microbiology resource announcements · 2021Article
- Microbial Communities Under Distinct Thermal and Geochemical Regimes in Axial and Off-Axis Sediments of Guaymas Basin.Frontiers in microbiology · 2021Article
- Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep.Nature communications · 2020Article
- Combined Use of Diagnostic Fumarate Addition Metabolites and Genes Provides Evidence for Anaerobic Hydrocarbon Biodegradation in Contaminated Groundwater.Microorganisms · 2020Article
- CoMA - an intuitive and user-friendly pipeline for amplicon-sequencing data analysis.PloS one · 2020Article
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Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present the MetaAmp pipeline for processing of SSU rRNA gene and other non-coding or protein-coding amplicon sequencing data by investigators that are inexperienced with bioinformatics procedures. It accepts single-end or paired-end sequences in fasta or fastq format from various sequencing platforms. It includes read quality control, and merging of forward and reverse reads of paired-end reads. It makes use of UPARSE, Mothur, and the SILVA database for clustering, removal of chimeric reads, taxonomic classification, and generation of diversity metrics. The pipeline has been validated with a mock community of known composition. MetaAmp provides a convenient web interface as well as command line interface. It is freely available at: http://ebg.ucalgary.ca/metaamp. Since its launch 2 years ago, MetaAmp has been used >2,800 times, by many users worldwide.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.