VIsoQLR

VIsoQLR analyzes and quantifies mRNA isoforms in selected genes from long-read sequencing to characterize splicing alterations caused by DNA variants.

Key Features:

• Dynamic splice-site adjustment and curation: Provides graphical and tabular representations enabling manual curation and adjustment of splice sites and isoform definitions.
• Semi-automated isoform identification and quantification: Detects and quantifies both known and novel isoforms from long-read sequencing data using semi-automated procedures.
• Reference-based alignment and consensus splice-site definition: Aligns sequences to a reference genome and defines consensus splice sites for each gene.
• Targeted gene-level analysis: Focuses analysis and visualization at the level of selected genes rather than whole-transcriptome profiling.
• Integration of external isoform annotations: Accepts imported known isoforms from other methods as references for comparison and validation.
• Benchmarking: Has been benchmarked against two popular transcriptome-based tools, demonstrating accurate performance in isoform detection and quantification.

Scientific Applications:

• Functional splicing assays: Analysis of isoform outcomes in patient cell lines or alternative models to validate the splicing impact of DNA variants.
• Targeted investigation of splicing-related genetic disease: Quantification and characterization of aberrant pre-mRNA splicing in genes implicated in human genetic disorders.

Methodology:

Processes aligned long-read sequencing reads (e.g., nanopore), aligns sequences to a reference genome, defines consensus splice sites per gene, performs semi-automated identification and quantification of known and novel isoforms, and accepts imported isoform references for comparison.