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Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines
Shotgun metagenomic sequencing comprehensively samples the DNA of a microbial sample. Choosing the best bioinformatics processing package can be...
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Full Shotgun DNA Metagenomics
Full DNA metagenomics is the sequencing of all DNA from a sample followed by assembly and annotation and assignment of sequence information to...
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Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients
BackgroundThe accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the...
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CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets
BackgroundShotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their...
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A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients
Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study the human gut microbiome. We previously compiled...
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Shotgun Metagenomic Approaches
The most recent advancements in the knowledge of sourdough ecologic meta-community come from the uncultured approach based on shotgun metagenomics...
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Shotgun Metagenomics Reveals Taxonomic and Functional Patterns of the Microbiome Associated with Barbour’s Seahorse (Hippocampus barbouri)
This study aimed to investigate the taxonomic and functional patterns of the microbiome associated with Barbour’s seahorse ( Hippocampus barbouri )...
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Genome characterization of a Turkish bovine rotavirus field isolate by shotgun metagenomics
A bovine rotavirus (BRV) isolate from Kirsehir was isolated from feces of a neonatal calf with diarrhea, identified, and sequenced by shotgun...
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Metagenomics Analysis of Sourdough Microbiota
The sourdough fermentation process is conducted by more than 50 bacterial genera, mostly homo and hetero-fermentative. In addition, over 35 yeasts...
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Unveiling the microbial diversity and functional dynamics of Shiv Kund, Sohna hot spring, India through a shotgun metagenomics approach
In this research, we examined the microbial diversity in Sohna hot spring, Haryana, India using shotgun metagenome sequencing based on the Illumina...
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Metagenomics Insight into the Mycobiome Analysis
The mycobiome, a subset of the microbiome focusing on fungal communities, encompasses a vast yet largely unidentified array of fungal species....
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Shotgun metagenomics and computational profiling of the plastisphere microbiome: unveiling the potential of enzymatic production and plastic degradation
Plastic pollution is one of the most resilient types of pollution and is considered a global environmental threat, particularly in the marine...
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Shallow shotgun sequencing reduces technical variation in microbiome analysis
The microbiome is known to play a role in many human diseases, but identifying key microbes and their functions generally requires large studies due...
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From Whole Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool
ViromeScan is an innovative metagenomic analysis tool that allows characterizing the taxonomy of viral communities from raw data of metagenomics...
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Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria
BackgroundOxford Nanopore Technologies (ONT) offers an accessible platform for long-read sequencing, which improves the reconstruction of genomes and...
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Methods to Study Metagenomics
Metagenomic profiling of human fecal samples has long uncovered the importance of the microbiota in human health and disease. In recent years,...
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Metagenomics Databases for Bacteria
The booming sequencing technologies have turned metagenomics into a widely used tool for microbe-related studies, especially in the areas of clinical...
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UMGAP: the Unipept MetaGenomics Analysis Pipeline
BackgroundShotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep...
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Microbial Metagenomics Developments for Environmental and Public Health Monitoring
Microbial metagenomics has transformed surveillance in the fields of community health and the environment by providing previously unobtainable...
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Unraveling metagenomics through long-read sequencing: a comprehensive review
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of...
