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Functional meta-omics provide critical insights into long- and short-read assemblies

Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artifacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only and hybrid assembly approaches on four different metagenomic samples of varying complexity. We de...

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Detalles Bibliográficos
Autores principales: Galata, Valentina, Busi, Susheel Bhanu, Kunath, Benoît Josef, de Nies, Laura, Calusinska, Magdalena, Halder, Rashi, May, Patrick, Wilmes, Paul, Laczny, Cédric Christian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8575027/
https://www.ncbi.nlm.nih.gov/pubmed/34453168
http://dx.doi.org/10.1093/bib/bbab330
Descripción
Sumario:Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artifacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only and hybrid assembly approaches on four different metagenomic samples of varying complexity. We demonstrate how different assembly approaches affect gene and protein inference, which is particularly relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic and metaproteomic data to assess the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions. We propose a reference-independent solution, which exploits the synergistic effects of multi-omic data integration for the in situ study of microbiomes using long-read sequencing data.