DRAP

DRAP improves de novo RNA-Seq transcriptome assemblies by integrating and post-processing Trinity and Oases outputs to reduce redundancy and correct chimera and nucleotide errors for organisms lacking a reference genome.

Key Features:

• Integration with established assemblers: Wraps and leverages Trinity and Oases assemblies to refine initial contig sets.
• Redundancy reduction: Reduces the number of resulting contigs by approximately 1.3- to 15-fold depending on dataset and assembler.
• Error correction: Addresses chimera formation and reduces nucleotide error rates in assembled contigs.
• Preservation of assembly quality metrics: Maintains read realignment rate and protein reconstruction counts while compacting assemblies.

Scientific Applications:

• Expression analysis without a reference genome: Produces compact transcript sets suitable for differential expression studies in non-model organisms.
• Gene expression profiling: Supplies refined contig sets for downstream quantification of transcript abundance.
• Novel transcript discovery: Facilitates identification of previously unannotated transcripts from de novo assemblies.
• Functional annotation of non-model organisms: Provides improved contig sets for downstream annotation and protein reconstruction.

Methodology:

DRAP wraps outputs from Trinity and Oases with additional processing steps aimed at contig compaction and error correction.