nf-core/denovotranscript: A Workflow for De Novo Transcriptome Assembly and Quantification of Paired-End Short Reads...

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• Bulk RNA sequencing (RNA-seq) is crucial for gene identification but requires a reference genome.
• De novo transcriptome assembly is challenging for organisms without a reference genome due to its complexity and resource demands.
• A standardized, reproducible workflow is needed to streamline this process.

Purpose of the Study:

• To introduce nf-core/denovotranscript, an open-source workflow for de novo transcriptome assembly and quantification.
• To provide a standardized and reproducible solution for analyzing RNA-seq data in the absence of a reference genome.
• To detail the workflow's capabilities, including pre-processing, assembly, redundancy reduction, quality assessment, and quantification.

Main Methods:

• The nf-core/denovotranscript workflow, built with Nextflow and the nf-core framework.
• Utilizes container technologies (Docker, Singularity, Podman) for portability.
• Covers the entire pipeline from raw RNA-seq data to quantified transcripts.

Main Results:

• The workflow facilitates de novo transcriptome assembly and quantification.
• It simplifies complex bioinformatics pipelines for non-model organisms.
• Offers portability across diverse computational environments through containerization.

Conclusions:

• nf-core/denovotranscript provides a robust, user-friendly solution for de novo transcriptome analysis.
• The workflow enhances accessibility and reproducibility in genomic research for non-model organisms.
• It addresses a critical need for standardized bioinformatics tools in transcriptomics.