Yanagi

Yanagi is a software tool that improves the efficiency and flexibility of RNA sequencing (RNA-seq) data analysis. It introduces a transcriptome segmentation approach that decouples the tasks of pseudo-alignment and transcript quantification, which are typically coupled in ultra-fast pseudo-alignment methods.

Key features of Yanagi:

1. Generates maximal disjoint segments from a transcriptome reference library, enabling ultra-fast pseudo-alignment to produce per-sample segment counts.

2. Allows direct usage of pseudo-alignment results in alternative splicing and differential gene expression analyses without the need for a separate transcript quantification step.

3. Utilizes segment counts, similar to other methods relying on local coverage statistics, providing an advantage over transcript quantification-based approaches in detecting and estimating local splicing when dealing with incomplete transcript annotations.

4. Exploits the computational and space efficiency of pseudo-alignment approaches while expanding their applicability and interpretability in various RNA-seq analyses.

5. Models and captures local coverage variation in RNA-seq analyses by using the transcriptome segmentation approach.