Reference : Functional meta-omics provide critical insights into long- and short-read assemblies
Scientific journals : Article
Life sciences : Microbiology
Systems Biomedicine
http://hdl.handle.net/10993/48171
Functional meta-omics provide critical insights into long- and short-read assemblies
English
Galata, Valentina mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
Busi, Susheel Bhanu mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
Kunath, Benoît mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
de Nies, Laura mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
Calusinska, Magdalena mailto [University of Luxembourg > > >]
Halder, Rashi mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Scientific Central Services >]
May, Patrick mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core >]
Wilmes, Paul mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
Laczny, Cedric Christian mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
27-Aug-2021
Briefings in Bioinformatics
Oxford University Press
Yes (verified by ORBilu)
International
1467-5463
1477-4054
United Kingdom
[en] third-generation sequencing ; long reads ; Oxford Nanopore Technologies ; hybrid assembly ; functional omics ; meta-omics
[en] 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.
Luxembourg Centre for Systems Biomedicine (LCSB)
Fonds National de la Recherche - FnR ; Swiss National Science Foundation ; European Research Council ; Probiotics in External Applications (PBGL)
Researchers ; Professionals ; Students
http://hdl.handle.net/10993/48171
10.1093/bib/bbab330
https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab330/6358409?login=true#294767762
Valentina Galata and Susheel Bhanu Busi Equal contribution.
© The Author(s) 2021. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
FnR ; FNR11823097 > Paul Wilmes > MICROH-DTU > Microbiomes In One Health > 01/09/2018 > 28/02/2025 > 2017

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