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Updated: May 2, 2026

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Published on: December 22, 2014
Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections
1Division of Microbiology and Infection,Warwick Medical School, University of Warwick,Coventry CV4 7AL,UK.
Abstract:
The term 'shotgun metagenomics' is applied to the direct sequencing of DNA extracted from a sample without culture or target-specific amplification or capture. In diagnostic metagenomics, this approach is applied to clinical samples in the hope of detecting and characterizing pathogens. Here, I provide a conceptual overview, before reviewing several recent promising proof-of-principle applications of metagenomics in virus discovery, analysis of outbreaks and detection of pathogens in contemporary and historical samples. I also evaluate future prospects for diagnostic metagenomics in the light of relentless improvements in sequencing technologies.
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