SplAdder

SplAdder augments genome annotations with RNA-Seq alignment evidence to identify, quantify, and test alternative splicing (AS) events for analyses of transcriptomic complexity.

Key Features:

• Annotation Augmentation: Incorporates RNA-Seq alignments and existing genome annotation to produce an augmented annotation reflecting observed transcriptomic evidence.
• Identification of Splicing Events: Detects alternative splicing events within the augmented annotation graph to pinpoint exon, intron, and junction-level AS events.
• Quantification and Confirmation: Quantifies identified AS events using RNA-Seq data and provides confirmation metrics based on alignment support.
• Statistical Analysis: Tests for significant quantitative differences between samples to identify differential splicing across conditions.

Scientific Applications:

• Novel transcript discovery in poorly annotated genomes: Detects AS events that reveal previously unannotated transcript variants in less well-annotated organisms.
• Disease-related splicing studies: Identifies and quantifies AS changes associated with disease states.
• Population-scale splicing variation: Analyzes differential splicing across large population studies to characterize transcriptomic diversity.
• Event-centric splicing analysis: Enables focused analysis of single splicing events rather than full transcript reconstruction for computational efficiency.

Methodology:

Leverages RNA-Seq alignments to augment genome annotations into an augmented annotation graph, then identifies and quantifies alternative splicing events from that graph and performs statistical tests for sample-to-sample differences.