Transcriptome assembly with rnaSPAdes
Current rule for rnaSPAdes includes multiple k-mers and uses --meta: https://git-r3lab.uni.lu/IMP/imp3/-/blob/master/workflow/rules/Assembly/single-omic/mt/metaspades.smk.
rnaSPAdes works using only a single k-mer size (automatically detected using read length by the default). We strongly recommend not to change this parameter.
rnaSPAdes is not compatible with other pipeline options such as --meta, --sc and --plasmid. If you wish to assemble metatranscriptomic data just run rnaSPAdes as it is.