nf‐core/denovotranscript: A Workflow for De Novo Transcriptome Assembly and Quantification of Paired‐End Short Reads from Bulk RNA‐Seq

Bulk RNA‐sequencing (RNA‐seq) is commonly used for identifying and characterizing genes through annotation, phylogeny, and differential expression analysis. For organisms without a reference genome, the need to generate a de novo transcriptome assembly for analyzing these data can prove challenging, as it is a multi‐step process requiring many tools and computational resources. Therefore, a standardized and reproducible workflow using current best practices is required. We introduce the nf‐core/denovotranscript workflow, an open‐source solution built using Nextflow and the nf‐core framework. The protocols here describe how the workflow can be used to perform pre‐processing, de novo transcriptome assembly, redundancy reduction, assembly quality assessment, and quantification using RNA‐seq 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.