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For organisms without a reference genome, the need to generate a\n                    <jats:italic>de novo<\/jats:italic>\n                    transcriptome assembly for analyzing these data can prove challenging, as it is a multi\u2010step process requiring many tools and computational resources. Therefore, a standardized and reproducible workflow using current best practices is required. We introduce the nf\u2010core\/denovotranscript workflow, an open\u2010source solution built using Nextflow and the nf\u2010core framework. The protocols here describe how the workflow can be used to perform pre\u2010processing,\n                    <jats:italic>de novo<\/jats:italic>\n                    transcriptome assembly, redundancy reduction, assembly quality assessment, and quantification using RNA\u2010seq data. This workflow offers simple installation and thorough documentation. The use of Docker, Singularity, and Podman container technologies also makes it portable across various computing environments. \u00a9 2025 Wiley Periodicals LLC.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Basic Protocol<\/jats:bold>\n                    : Running nf\u2010core\/denovotranscript for\n                    <jats:italic>de novo<\/jats:italic>\n                    transcriptome assembly and quantification\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>Support Protocol<\/jats:bold>\n                    : Installation and configuration for command line usage\n                  <\/jats:p>","DOI":"10.1002\/cpz1.70248","type":"journal-article","created":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T16:38:22Z","timestamp":1763138302000},"source":"Crossref","is-referenced-by-count":2,"title":["nf\u2010core\/denovotranscript: A Workflow for\n                    <i>De Novo<\/i>\n          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Queensland  St Lucia QLD Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomer","family":"Ventura","sequence":"additional","affiliation":[{"name":"Centre for Bioinnovation University of the Sunshine Coast  Sippy Downs QLD Australia"},{"name":"School of Science, Technology and Engineering University of the Sunshine Coast  Sippy Downs QLD Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2025,11,14]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/S41598\u2010023\u201039620\u20106"},{"key":"e_1_2_8_3_1","unstructured":"Andrews S.(2010).Babraham Bioinformatics \u2010 FastQC A Quality Control Tool for High Throughput Sequence 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F.(2023).nf\u2010core\/differentialabundance: V1.4.0 \u2010 2023\u201011\u201027(1.4.0).Zenodo.https:\/\/doi.org\/10.5281\/zenodo.10209675"}],"container-title":["Current Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cpz1.70248","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T12:49:07Z","timestamp":1764938947000},"score":1,"resource":{"primary":{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/10.1002\/cpz1.70248"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11]]},"references-count":40,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2025,11]]}},"alternative-id":["10.1002\/cpz1.70248"],"URL":"https:\/\/doi.org\/10.1002\/cpz1.70248","archive":["Portico"],"relation":{},"ISSN":["2691-1299","2691-1299"],"issn-type":[{"value":"2691-1299","type":"print"},{"value":"2691-1299","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11]]},"article-number":"e70248"}}