TransBorrow

TransBorrow integrates assemblies from multiple transcriptome assemblers to perform genome-guided reconstruction of transcripts from RNA-seq data.

Key Features:

• Genome-guided transcriptome assembly: Performs transcript reconstruction in a genome-guided framework using RNA-seq data.
• Borrowing assemblies: Integrates assemblies produced by multiple existing assemblers to construct a comprehensive assembly resource.
• Colored graph construction: Builds a colored graph where each color corresponds to a specific assembler to represent and compare assembled subsequences.
• Reliable subsequence identification: Identifies reliable subsequences from the integrated assemblies for seeding downstream assembly steps.
• Path extension strategy: Seeds reliable subsequences into a splicing graph and extends paths to search for transcript-representing paths covering splicing events.
• Performance evaluation: Has been evaluated on simulated and real datasets to assess assembly quality relative to other transcriptome assemblers.

Scientific Applications:

• Transcriptome reconstruction: Reconstruction of full-length transcripts and isoforms from RNA-seq data.
• Alternative splicing analysis: Detection and characterization of alternative splicing events through splicing-graph-based path discovery.
• Gene expression and isoform discovery: Improved identification of expressed isoforms for downstream gene expression analyses.
• Post-transcriptional modification studies: Support for investigations into transcript diversity relevant to post-transcriptional regulation.

Methodology:

Integrates assemblies from multiple assemblers, constructs a colored graph to identify reliable subsequences, seeds those subsequences into a splicing graph, and applies a path extension strategy to search for transcript-representing paths; evaluated on simulated and real RNA-seq datasets.