Coral

Coral bridges paired-end RNA-seq reads to reconstruct full RNA fragment alignments and improve transcript assembly accuracy.

Key Features:

• Optimization Formulation: Employs an optimization formulation to identify the most reliable bridging path between paired-end reads while filtering out false paths.
• Dynamic Programming Algorithm: Uses a dynamic programming algorithm to compute the top N optimal bridging solutions.
• Consensus Approach: Selects the final bridging path via a consensus method that considers the fragment length distribution.
• Modularity: Modular design enables integration into existing RNA-seq analysis pipelines.

Scientific Applications:

• Transcript assembly improvement: In evaluations on 2377 GTEx RNA-seq samples, incorporating Coral with StringTie increased adjusted precision by 7.5% and with Scallop by 11.2%.
• Effective read extension: Extends the effective length of RNA-seq reads to support more comprehensive downstream transcriptomic analyses.

Methodology:

Formulates bridging as an optimization problem, solves it with a dynamic programming algorithm to obtain the top N solutions, applies a consensus approach using fragment length distribution, and filters false paths.