cloudrnaSPAdes

cloudrnaSPAdes assembles full-length isoforms from barcoded RNA sequencing (RNA-seq) linked-read data in a reference-free manner to reconstruct transcriptomes and enable novel isoform discovery.

Key Features:

• Barcoded linked-reads: Utilizes barcoded short-read RNA data where each barcode links reads originating from the same RNA molecule to enable reconstruction of full-length transcripts.
• Reference-free assembly: Operates without a reference genome or transcriptome, supporting novel isoform discovery and analyses in poorly annotated organisms.
• Handling coverage gaps: Manages coverage gaps within molecules by assembling isoforms per barcode to maintain accurate reconstruction despite uneven read distribution.
• High isoform diversity: Capable of reconstructing complex transcriptomes and handling genes with high isoform diversity, as demonstrated on simulated and real human data sets.
• SPAdes-based framework: Builds upon the SPAdes assembler framework with RNA-seq-specific enhancements to process barcoded linked-reads.

Scientific Applications:

• Novel isoform discovery: Enables discovery of previously unannotated transcript isoforms by linking reads from the same molecule to achieve effective full-length assembly.
• Reference-free transcriptomic studies: Supports investigation of gene expression patterns and alternative splicing without relying on reference-based methods.

Methodology:

cloudrnaSPAdes builds upon the SPAdes assembler framework and processes barcoded linked-reads to determine expressed isoforms per barcode, incorporating RNA-seq-specific enhancements.