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The majority of these organisms lack a well-annotated reference genome to serve as a basis for studying differentially expressed genes (DEGs). As an alternative cost-effective protocol to using a reference genome, the assembly of RNA-seq raw reads is performed to produce what is referred to as a \u2018de novo transcriptome,\u2019 serving as a reference for subsequent DEGs\u2019 analysis. This assembly step for conventional DEGs analysis pipelines for non-model organisms is a computationally expensive task. Furthermore, the complexity of the de novo transcriptome assembly workflows poses a challenge for researchers in implementing best-practice techniques and the most recent software versions, particularly when applied to various organisms of interest.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>To address computational challenges in transcriptomic analyses of non-model organisms, we present HPC-T-Assembly, a tool for de novo transcriptome assembly from RNA-seq data on high-performance computing (HPC) infrastructures. It is designed for straightforward setup via a Web-oriented interface, allowing analysis configuration for several species. Once configuration data is provided, the entire parallel computing software for assembly is automatically generated and can be launched on a supercomputer with a simple command line. Intermediate and final outputs of the assembly pipeline include additional post-processing steps, such as assembly quality control, ORF prediction, and transcript count matrix construction.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>HPC-T-Assembly allows users, through a user-friendly Web-oriented interface, to configure a run for simultaneous assemblies of RNA-seq data from multiple species. The parallel pipeline, launched on HPC infrastructures, significantly reduces computational load and execution times, enabling large-scale transcriptomic and meta-transcriptomics analysis projects.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/s12859-025-06121-4","type":"journal-article","created":{"date-parts":[[2025,4,28]],"date-time":"2025-04-28T14:23:23Z","timestamp":1745850203000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets"],"prefix":"10.1186","volume":"26","author":[{"given":"Franco","family":"Liberati","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taiel Maximiliano","family":"Pose Marino","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paolo","family":"Bottoni","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniele","family":"Canestrelli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tiziana","family":"Castrignan\u00f2","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,4,28]]},"reference":[{"issue":"1","key":"6121_CR1","doi-asserted-by":"publisher","first-page":"e59","DOI":"10.1002\/cpmb.59","volume":"122","author":"BE Slatko","year":"2018","unstructured":"Slatko BE, Gardner AF, Ausubel FM. 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