{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:04Z","timestamp":1753875844627,"version":"3.41.2"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T00:00:00Z","timestamp":1739923200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The Sequencing Read Archive is one of the largest and fastest-growing repositories of sequencing data, containing tens of petabytes of sequenced reads. Its data is used by a wide scientific community, often beyond the primary study that generated them. Such analyses rely on accurate metadata concerning the type of experiment and library, as well as the organism from which the sequenced reads were derived. These metadata are typically entered manually by contributors in an error-prone process, and are frequently incomplete. In addition, easy-to-use computational tools that verify the consistency and completeness of metadata describing the libraries to facilitate data reuse, are largely unavailable. Here, we introduce HTSinfer, a Python-based tool to infer metadata directly and solely from bulk RNA-sequencing data generated on Illumina platforms. HTSinfer leverages genome sequence information and diagnostic genes to rapidly and accurately infer the library source and library type, as well as the relative read orientation, 3\u2032 adapter sequence and read length statistics. HTSinfer is written in a modular manner, published under a permissible free and open-source license and encourages contributions by the community, enabling easy addition of new functionalities, e.g. for the inference of additional metrics, or the support of different experiment types or sequencing platforms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>HTSinfer is released under the Apache License 2.0. Latest code is available via GitHub at https:\/\/github.com\/zavolanlab\/htsinfer, while releases are published on Bioconda. A snapshot of the HTSinfer version described in this article was deposited at Zenodo at 10.5281\/zenodo.13985958.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf076","type":"journal-article","created":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T16:41:31Z","timestamp":1739983291000},"source":"Crossref","is-referenced-by-count":0,"title":["HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-3932-3964","authenticated-orcid":false,"given":"M\u00e1t\u00e9","family":"Balajti","sequence":"first","affiliation":[{"name":"Biozentrum, University of Basel , Basel 4056,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics , Lausanne 1015,","place":["Switzerland"]}]},{"given":"Rohan","family":"Kandhari","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel , Basel 4056,","place":["Switzerland"]}]},{"given":"Boris","family":"Juri\u010d","sequence":"additional","affiliation":[{"name":"Institute of Computer Science, Masaryk University , Brno 60200,","place":["Czech Republic"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8832-2041","authenticated-orcid":false,"given":"Mihaela","family":"Zavolan","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel , Basel 4056,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics , Lausanne 1015,","place":["Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3468-0652","authenticated-orcid":false,"given":"Alexander","family":"Kanitz","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel , Basel 4056,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics , Lausanne 1015,","place":["Switzerland"]}]}],"member":"286","published-online":{"date-parts":[[2025,2,19]]},"reference":[{"key":"2025030810261109500_btaf076-B1","doi-asserted-by":"crossref","first-page":"2056","DOI":"10.1021\/acs.jproteome.0c00904","article-title":"BioContainers registry: Searching bioinformatics and proteomics tools, packages, and containers","volume":"20","author":"Bai","year":"2021","journal-title":"J Proteome Res"},{"year":"2024","author":"Balajti","key":"2025030810261109500_btaf076-B2"},{"year":"2024","author":"Balajti","key":"2025030810261109500_btaf076-B3"},{"key":"2025030810261109500_btaf076-B4","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.sbi.2014.01.002","article-title":"A new system for naming ribosomal proteins","volume":"24","author":"Ban","year":"2014","journal-title":"Curr Opin Struct Biol"},{"key":"2025030810261109500_btaf076-B5","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat Biotechnol"},{"key":"2025030810261109500_btaf076-B6","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"year":"2013","author":"European Organization For Nuclear Research. 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