TGStools

TGStools enables comprehensive analysis of transcriptomes from long-read third-generation sequencing by characterizing full-length transcripts, detecting alternative splicing (including shifted types), identifying long noncoding RNAs (lncRNAs), and prioritizing transcripts through integration of annotation with genomic features.

Key Features:

• Full-length transcript characterization: Accurately characterizes full-length transcripts from long-read sequencing data to resolve transcript isoforms.
• Alternative splicing detection: Detects various alternative splicing events, explicitly including shifted splicing types that can be missed by traditional methods.
• lncRNA identification: Identifies long noncoding RNAs (lncRNAs) within the transcriptome.
• Transcript prioritization and visualization: Integrates rich annotation data with known genomic features to prioritize transcripts and support visualization-based assessment.
• Long-read/third-generation sequencing compatibility: Operates on data derived from third-generation long-read sequencing, including reads spanning several thousand base pairs.

Scientific Applications:

• Rare Mendelian disease research: Supports discovery of novel isoforms and lncRNAs relevant to rare Mendelian disease investigations.
• Transcript diversity and regulation studies: Enables analysis of transcript diversity and splicing regulation through comprehensive alternative splicing detection.
• Functional genomics and gene expression: Facilitates understanding of gene expression patterns by resolving full-length transcript structures.
• Prioritization for experimental follow-up: Guides selection of transcripts for downstream functional studies by integrating annotations and genomic feature context.

Methodology:

Processes long-read third-generation sequencing data to characterize full-length transcripts, detect alternative splicing events including shifted types, identify lncRNAs, and integrate annotation with genomic features for transcript prioritization and visualization.