While RNA-Seq is commonly used for model organisms with well-known genomes, multiple projects study species with previously unsequenced genome. Since finishing a genome can be costly and challenging (especially when the genome is large), RNA-Seq can be used for the purpose of de novo transcriptome assembly. Due to varying expression levels of different isoforms and genes, RNA-Seq data sets are characterized by highly uneven coverage depth — a problem that was successfully addressed by SPAdes genome assembler. rnaSPAdes is a SPAdes tool, modified and tuned for assembling transcripts from RNA-Seq data.


Download: rnaSPAdes is distributed as a part of SPAdes assembler.