CircSeqAlignTk

CircSeqAlignTk provides end-to-end analysis of RNA-seq data for circular genomes, particularly for studying organisms such as viroids with circular RNA genomes of 246-401 nucleotides.

Key Features:

• Alignment to circular genomes: Performs RNA-seq read alignment specifically optimized for circular genome sequences.
• Visualization of circular genomes: Generates visualizations of circular genome sequences from aligned RNA-seq data.
• Synthetic sequencing data generation: Produces synthetic RNA-seq data that mirrors real RNA-seq data from biological experiments for method evaluation.
• Workflow evaluation framework: Enables developers to evaluate the performance of alignment tools and new workflows for circular genome analysis.

Scientific Applications:

• Viroid infection mechanism research: Supports transcriptome-level study of viroids, circular RNA pathogens that infect plants and cause economic and agricultural damage.
• Circular genome transcriptomics: Facilitates RNA-seq-based analysis of gene expression and biological mechanisms in organisms with circular genomes.
• Alignment tool benchmarking: Allows computational evaluation and comparison of alignment methods using realistic synthetic data.

Methodology:

CircSeqAlignTk implements end-to-end RNA-seq data analysis through a series of functions spanning alignment to visualization of circular genome sequences. The synthetic data generation feature creates artificial sequencing data that mirrors real RNA-seq data from biological experiments.