Necklace

Necklace constructs a superTranscriptome by integrating genome-guided and de novo RNA-seq transcript assemblies with reference genome annotations to enable comprehensive transcriptomic analyses.

Key Features:

• SuperTranscriptome construction: Builds a unified superTranscriptome by amalgamating assembled transcripts with annotated transcripts from reference genomes.
• Assembly integration: Integrates genome-guided and de novo transcriptome assemblies to capture transcripts from multiple assembly strategies.
• Read alignment to superTranscriptome: Aligns RNA-seq reads to the constructed superTranscriptome to generate mappings for downstream analysis.
• Novel transcript detection: Captures both known and novel transcripts to improve transcriptome completeness for species with incomplete genomes or annotations.
• Differential expression support: Produces a reference suitable for standard differential expression testing.

Scientific Applications:

• Comprehensive transcriptome reconstruction: Produces a more complete transcriptome representation by combining assembled and annotated transcripts.
• Differential expression analysis: Enables downstream differential expression testing using reads aligned to the superTranscriptome.
• Novel transcript discovery: Identifies transcripts absent from existing reference annotations.
• Analyses of species with incomplete genomes or annotations: Facilitates transcriptomic studies when reference genomes are incomplete or unavailable.
• Gene expression profiling: Improves detection and interpretation of gene expression patterns across samples.

Methodology:

Runs genome-guided and de novo transcriptome assemblies, merges assembled transcripts with reference genome annotations to build a superTranscriptome, and aligns RNA-seq reads to that superTranscriptome to prepare data for differential expression testing.