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However, working with and especially curating public omics datasets remains challenging despite these efforts. While a growing number of initiatives aim to re-use previous results, these present limitations that often lead to the need for further in-house curation and processing.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Here, we present the Omics Dataset Curation Toolkit (OMD Curation Toolkit), a python3 package designed to accompany and guide the researcher during the curation process of metadata and fastq files of public omics datasets. This workflow provides a standardized framework with multiple capabilities (collection, control check, treatment and integration) to facilitate the arduous task of curating public sequencing data projects. While centered on the European Nucleotide Archive (ENA), the majority of the provided tools are generic and can be used to curate datasets from different sources.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Thus, it offers valuable tools for the in-house curation previously\u00a0needed to re-use public omics data. Due to its workflow structure and capabilities, it can be easily used and benefit investigators in developing novel omics meta-analyses based on sequencing data.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-024-05803-9","type":"journal-article","created":{"date-parts":[[2024,5,9]],"date-time":"2024-05-09T18:02:49Z","timestamp":1715277769000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["OMD Curation Toolkit: a workflow for in-house curation of public omics datasets"],"prefix":"10.1186","volume":"25","author":[{"given":"Samuel","family":"Piquer-Esteban","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vicente","family":"Arnau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wladimiro","family":"Diaz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9s","family":"Moya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,9]]},"reference":[{"key":"5803_CR1","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.plantsci.2017.10.014","volume":"267","author":"P Bhandary","year":"2018","unstructured":"Bhandary P, Seetharam AS, Arendsee ZW, Hur M, Wurtele ES. Raising orphans from a metadata morass: a researcher\u2019s guide to re-use of public \u2019omics data. Plant Sci. 2018;267:32\u201347.","journal-title":"Plant Sci"},{"key":"5803_CR2","doi-asserted-by":"publisher","first-page":"2872","DOI":"10.3390\/nu14142872","volume":"14","author":"I Sharon","year":"2022","unstructured":"Sharon I, Quijada NM, Pasolli E, Fabbrini M, Vitali F, Agamennone V, et al. The core human microbiome: does it exist and how can we find it? A critical review of the concept. Nutrients. 2022;14:2872.","journal-title":"Nutrients"},{"key":"5803_CR3","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03751-6","author":"A Lachmann","year":"2018","unstructured":"Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, et al. Massive mining of publicly available RNA-seq data from human and mouse. 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