HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets
Author(s)
Liberati, Franco
Pose Marino, Taiel Maximiliano
Bottoni, Paolo
Date Issued
2025
Type
article
Volume
26
Issue
1
Start Page
113
Journal
Abstract
Recent years have seen a substantial increase in RNA-seq data production, with this technique becoming the primary approach for gene expression studies across a wide range of non-model organisms. 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 'de novo transcriptome,' serving as a reference for subsequent DEGs' 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.