What it does
SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
rnaSPAdes is a subtool for de novo transcriptome assembly from RNA-Seq data and is suitable for all kinds of organisms.
rnaSPAdes take as an input at least one paired-end or single-end library. For hybrid assembly you can use PacBio or Oxford Nanopore reads.
In case you have sequenced several RNA-Seq libraries using the same protocol from different tissues / conditions, and the goal as to assemble a total transcriptome, we suggest to provide all files as a single library. Note, that sequencing using the same protocol implies that the resulting reads have the same length, insert size and strand-specificity. Transcript quantification for each sample can be done afterwards by separately mapping reads from each library to the assembled transcripts.
More information can be found on on github.