Evaluating the information content of shallow shotgun metagenomics

B Hillmann, GA Al-Ghalith, RR Shields-Cutler, Q Zhu…�- Msystems, 2018 - Am Soc Microbiol
Although microbial communities are associated with human, environmental, plant, and
animal health, there exists no cost-effective method for precisely characterizing species and�…

[HTML][HTML] Shallow shotgun sequencing reduces technical variation in microbiome analysis

AJ La Reau, NB Strom, E Filvaroff, K Mavrommatis…�- Scientific reports, 2023 - nature.com
The microbiome is known to play a role in many human diseases, but identifying key
microbes and their functions generally requires large studies due to the vast number of�…

[HTML][HTML] Characterization of shallow whole-metagenome shotgun sequencing as a high-accuracy and low-cost method by complicated mock microbiomes

W Xu, T Chen, Y Pei, H Guo, Z Li, Y Yang…�- Frontiers in�…, 2021 - frontiersin.org
Characterization of the bacterial composition and functional repertoires of microbiome
samples is the most common application of metagenomics. Although deep whole�…

[HTML][HTML] Benchmarking second and third-generation sequencing platforms for microbial metagenomics

V Meslier, B Quinquis, K Da Silva, F Plaza O�ate…�- Scientific Data, 2022 - nature.com
Shotgun metagenomic sequencing is a common approach for studying the taxonomic
diversity and metabolic potential of complex microbial communities. Current methods�…

Quantitative assessment of shotgun metagenomics and 16S rDNA amplicon sequencing in the study of human gut microbiome

I Laudadio, V Fulci, F Palone, L Stronati…�- OMICS: A Journal of�…, 2018 - liebertpub.com
The analysis of microbiota composition in humans, animals, and built environments is
important because of emerging roles and applications in a broad range of disease and�…

[HTML][HTML] MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

GV Uritskiy, J DiRuggiero, J Taylor�- Microbiome, 2018 - Springer
Background The study of microbiomes using whole-metagenome shotgun sequencing
enables the analysis of uncultivated microbial populations that may have important roles in�…

Shotgun metagenomics, from sampling to analysis

C Quince, AW Walker, JT Simpson, NJ Loman…�- Nature�…, 2017 - nature.com
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are�…

[HTML][HTML] Toward accurate and quantitative comparative metagenomics

S Nayfach, KS Pollard�- Cell, 2016 - cell.com
Shotgun metagenomics and computational analysis are used to compare the taxonomic and
functional profiles of microbial communities. Leveraging this approach to understand roles of�…

[PDF][PDF] Assessment of fecal DNA extraction protocols for metagenomic studies

F Yang, J Sun, H Luo, H Ren, H Zhou, Y Lin…�- …, 2020 - academic.oup.com
Background Shotgun metagenomic sequencing has improved our understanding of the
human gut microbiota. Various DNA extraction methods have been compared to find�…

Accessible, curated metagenomic data through ExperimentHub

E Pasolli, L Schiffer, P Manghi, A Renson…�- Nature�…, 2017 - nature.com
To the Editor: The microbiome has emerged as a key aspect of human biology and has been
implicated in many disease etiologies. Shotgun metagenomic sequencing is an approach�…