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Automation of QIIME2 Metagenomic Analysis Platform
Current Protocols, 2021AbstractQIIME is a widely used, open‐source microbiome analysis software package that converts raw sequence data into interpretable visualizations and statistical results. QIIME2 has recently succeeded QIIME1, becoming the most updated platform. The protocols in this article describe our effort in automating core functions of QIIME2, using datasets ...
Calvin, Fung +6 more
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2010
The term “metagenomics” represents a combination of molecular and bioinformatic tools used to assess the genetic information of a community without prior cultivation of the individual species. It is valuable for the study of microorganisms of which only a minor fraction is yet culturable.
Meyerdierks, A., Glöckner, F.
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The term “metagenomics” represents a combination of molecular and bioinformatic tools used to assess the genetic information of a community without prior cultivation of the individual species. It is valuable for the study of microorganisms of which only a minor fraction is yet culturable.
Meyerdierks, A., Glöckner, F.
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In Silico Metagenomics Analysis
2021The field of metagenomics (study of a system’s microbiome) comes with various questions researchers are called to answer. Questions about the microbiota’s identity, the interactions of the participating bacteria, fungi, and viruses and their associations with health and disease.
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METAGENOME ANALYSIS USING MEGAN
Proceedings of the 5th Asia-Pacific Bioinformatics Conference, 2007In metagenomics, the goal is to analyze the genomic content of a sample of organisms collected from a common habitat. One approach is to apply large-scale random shotgun sequencing techniques to obtain a collection of DNA reads from the sample. This data is then compared against databases of known sequences such as NCBI-nr or NCBI-nt, in an attempt to ...
DANIEL H. HUSON +3 more
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Diversity Analysis in Viral Metagenomes
2018Viruses are the most abundant and diverse biological entity in the earth. Nowadays, there are several viral metagenomes from different ecological niches which have been used to characterize new viral particles and to determine their diversity. However, viral metagenomic data have the disadvantage to be high-dimensional compositional and sparse.
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2014
In this chapter, we first briefly introduce the background of next-generation sequencing metagenomics, including the special properties in this research field and the challenges for statistical analysis. A metagenomic study typically consists of sampling, filtering, DNA extraction, sequencing, binning, assembly, profiling and down-stream analysis.
Ruofei Du, Zhide Fang
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In this chapter, we first briefly introduce the background of next-generation sequencing metagenomics, including the special properties in this research field and the challenges for statistical analysis. A metagenomic study typically consists of sampling, filtering, DNA extraction, sequencing, binning, assembly, profiling and down-stream analysis.
Ruofei Du, Zhide Fang
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Workflow for Rapid Metagenome Analysis
2014Analyses of metagenomes in life sciences present new opportunities as well as challenges to the scientific community and call for advanced computational methods and workflows. The large amount of data collected from samples via next-generation sequencing (NGS) technologies render manual approaches to sequence comparison and annotation unsuitable ...
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2019
In this chapter, we learn how to use the metagenomeSeq in the R package for both metadata and functional analyses of metagenomes using published data. It includes preprocessing and annotation methods such as gene-centered, pathway-centered, and functional diversity analyses.
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In this chapter, we learn how to use the metagenomeSeq in the R package for both metadata and functional analyses of metagenomes using published data. It includes preprocessing and annotation methods such as gene-centered, pathway-centered, and functional diversity analyses.
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Metagenomics: Genomic Analysis of Microbial Communities
Annual Review of Genetics, 2004▪ Abstract Uncultured microorganisms comprise the majority of the planet's biological diversity. Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques ...
Christian S, Riesenfeld +2 more
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