Isoform discovery in long-read sequencing: Tuning computational pipeline

Isoform determination is crucial for understanding the functional diversity of proteins. However, obtaining high-quality sequencing data and optimizing bioinformatics tools for upstream analysis can be challenging. In this study, we present the optimization of a selected software pipeline using the Spike-In RNA Variant (SIRV) standard kit, which contains a diverse set of synthetic isoforms that mimic transcriptome complexity. SIRV data serves as a gold standard, enabling parameter tuning of software tools based on these synthetic reads. We applied the optimized pipeline to long-read sequencing data generated from the same SIRV molecular biology kit to enhance isoform detection capabilities. Our results highlight the importance of parameter optimization and demonstrate the advantages of long-read sequencing in resolving complex isoform structures. This approach offers improved accuracy in isoform identification, contributing to a more comprehensive understanding of protein diversity and function.