RNA-Seq is vastly used for well-studied organisms such as mouse and human, thus allowing to use reference-based methods for the analysis. However, multiple research projects study organisms with previously unsequenced genomes therefore creating a need for de novo transcriptome assembler. Due to varying expressions levels of different genes and isoforms, RNA-Seq data sets are characterized by highly-uneven coverage depth. Since SPAdes assembler is already capable of dealing with non-uniform coverage (typical for single-cell genomic data), we have decided to create rnaSPAdes — a SPAdes-based assembler for RNA-Seq data.
In addition, we complement it with rnaQUAST — a quality assessment tool for transcriptome assemblers, which works for both — model organisms with reference genome and gene database, and organisms whose genome is unknown.
