CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool

Traditional short-read RNA-Seq analysis pipelines predominantly focus on protein-coding genes, often overlooking other genomic sequences such as transposable elements (TEs) and non-coding RNA dynamics and do not usually investigate splicing events or transcript usage. To fully capture the complexity of the transcriptome, and in particular transcriptomic regulation, it is crucial to adopt a comprehensive approach that integrates these diverse aspects, providing a more complete and nuanced understanding of expression dynamics in the studied organism.

To address these limitations, we present CRESCENT (Comprehensive RNA-seq Expression, Splicing, and Coding/non-coding Element Network Tool), a Snakemake workflow capable of performing a fully automated and comprehensive RNA-Seq analysis. CRESCENT integrates multiple tools at each step of the workflow and enables analysis of differential expression, differential alternative splicing, differential transcript usage, and gene ontology-based functional enrichment for all three. The workflow takes advantage of multiple Snakemake wrappers to minimize required installations for the user, integrating the latest versions of popular bioinformatic tools. It can be run for a complete analysis or for only a specific part in accordance with the configuration file provided by the user. The CRESCENT workflow was validated, demonstrating the pipeline's reliability, as differentially expressed protein-coding genes, TEs and differential alternative splicing events were consistent with previously published datasets. Finally, benchmarking CRESCENT performance indicated that it can be run on a personal computer or a remote server, including a high-performance computing cluster, allowing a user to process small single-end sequencing on species possessing a small genome like Arabidopsis thaliana to very large paired-end sequencing on polyploid species like wheat.

CRESCENT is a scalable solution for comprehensive transcriptomic profiling. It is freely available at https://github.com/gilless429/crescent .