CRAC

CRAC analyzes RNA-Seq reads to detect mutations, insertions and deletions (indels), splice junctions, and fusion RNAs using a k-mer–based profiling approach.

Key Features:

• k-mer Profiling Analysis: Uses k-mer–based profiling of RNA-Seq reads to identify candidate mutations, indels, splice junctions, and chimeric junctions.
• Alignment-Free Variant Detection: Detects genetic alterations directly from RNA-Seq read analysis without requiring a preliminary alignment step.
• Splice and Fusion Detection: Identifies splice junctions and fusion RNAs, including novel recurrent chimeric junctions.
• Coverage-Aware Prediction: Integrates genomic location information with local read coverage to improve prediction precision.

Scientific Applications:

• Cancer Transcriptomics: Detects mutations, indels, splice junctions, and fusion transcripts in cancer RNA-Seq datasets.
• Transcriptome Analysis: Supports identification of transcript variants and RNA rearrangements from high-throughput RNA sequencing.
• Gene Fusion Discovery: Enables detection of validated and novel fusion RNAs in transcriptomic data.

Methodology:

CRAC performs k-mer profiling of RNA-Seq reads to identify sequence variations and junction signals, integrates genomic location and local coverage information, and predicts mutations, indels, splice junctions, and chimeric junctions directly from read analysis.