Bellerophon

Bellerophon identifies and removes chimeric sequences from de novo transcriptome assemblies to improve the accuracy of RNA-Seq–based transcriptomic analyses.

Key Features:

• Chimera Detection and Removal: Identifies and eliminates chimeric contigs in de novo assembled transcriptomes.
• Quality Assessment Integration: Incorporates TransRate to evaluate initial assembly quality.
• Expression-Based Filtering: Applies a transcripts per million (TPM) filter to remove lowly expressed contigs.
• Redundancy Reduction: Uses CD-HIT-EST to remove highly identical contigs and reduce redundancy.
• Chimera Validation and Benchmarking: Validated via computational chimera creation, identification in existing assemblies, and simulated RNA-Seq using known reference transcriptomes, reporting chimera removal rates between 40% and 91.9%.

Scientific Applications:

• De novo RNA-Seq assembly quality control: Improves assembly fidelity when a reference genome is unavailable.
• Comparative genomics: Enhances the reliability of cross-species transcript comparisons by reducing assembly artifacts.
• Evolutionary biology: Supports studies that require accurate transcript sequences for evolutionary inference.
• Functional genomics and gene expression analysis: Provides higher-fidelity transcriptomes for downstream expression and functional analyses.

Methodology:

Initial assembly quality is assessed with TransRate; lowly expressed contigs are removed using a TPM filter; redundancy is reduced with CD-HIT-EST; validation is performed via computational chimera creation, identification in existing assemblies, and simulated RNA-Seq using known reference transcriptomes.