Synergistic effect of short- and long-read sequencing on functional meta-omics [* Cross-Reference *]

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Valentina Galata; Susheel Bhanu Busi; Benoît J. Kunath; Laura de Nies; Magdalena Całusińska; Rashi Halder; Patrick May; Paul Wilmes; Cédric C. Laczny, 2026, "Synergistic effect of short- and long-read sequencing on functional meta-omics [* Cross-Reference *]", https://lore.list.lu/citation?persistentId=perma:LIST.GISSNR, LIST Open Repository, V1

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Description	Abstract Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artefacts 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 and demonstrate how they 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 evaluate the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions and we propose a reference-independent solution based on the synergistic effects of multi-omic data integration for the in situ study of microbiomes using long-read sequencing data. (2021-04-23) *This entry has been automatically imported via OpenAlex by LIST harvest scripts. Please refer to https://doi.org/10.1101/2021.04.22.440869 for the original and latest version of the publication* (2026-07-01)
Subject	Chemistry; Medicine, Health and Life Sciences
Keyword	Metagenomics, Computational biology, Microbiome, Biology, Inference, Computer science, Gene, Bioinformatics, Artificial intelligence, Genetics
License/Data Use Agreement	CC BY 4.0


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Citation Metadata

Persistent Identifier	perma:LIST.GISSNR
Publication Date	2026-07-06
Title	Synergistic effect of short- and long-read sequencing on functional meta-omics [* Cross-Reference *]
Other Identifier	https://doi.org/10.1101/2021.04.22.440869 OpenAlex ID: https://openalex.org/W3158976456
Author	Valentina Galata - ORCID: https://orcid.org/0000-0002-4541-427X Susheel Bhanu Busi - ORCID: https://orcid.org/0000-0001-7559-3400 Benoît J. Kunath - ORCID: https://orcid.org/0000-0002-3356-8562 Laura de Nies - ORCID: https://orcid.org/0000-0002-6483-7489 Magdalena Całusińska (Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0003-2270-2217 Rashi Halder - ORCID: https://orcid.org/0000-0002-1402-1254 Patrick May - ORCID: https://orcid.org/0000-0001-8698-3770 Paul Wilmes - ORCID: https://orcid.org/0000-0002-6478-2924 Cédric C. Laczny - ORCID: https://orcid.org/0000-0002-1100-1282
Point of Contact	Use email button above to contact. LIST QDKM (LIST)
Description	Abstract Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artefacts 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 and demonstrate how they 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 evaluate the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions and we propose a reference-independent solution based on the synergistic effects of multi-omic data integration for the in situ study of microbiomes using long-read sequencing data. (2021-04-23) *This entry has been automatically imported via OpenAlex by LIST harvest scripts. Please refer to https://doi.org/10.1101/2021.04.22.440869 for the original and latest version of the publication* (2026-07-01)
Subject	Chemistry; Medicine, Health and Life Sciences
Keyword	Metagenomics Computational biology Microbiome Biology Inference Computer science Gene Bioinformatics Artificial intelligence Genetics
Topic Classification	Genomics and Phylogenetic Studies Gut microbiota and health Bioinformatics and Genomic Networks
Deposit Date	2021-04-23
Data Type	Preprint
Data Source	bioRxiv (Cold Spring Harbor Laboratory)

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